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Farmers in Nepal face many of the same global challenges associated with initiating and scaling poultry husbandry as many other developing countries. These include access to innovative approaches in finance, credit, coop design, marketing, and sales. As with most low-income countries, Nepalese poultry farmers also lack adequate training in poultry husbandry including biosecurity. In this paper, we describe a collaborative workshop-subsidy approach to addressing these challenges conducted by a partnership with the UC Davis School of Veterinary Medicine, the College of Engineering, the School of Education, and a farming co-operative based in the semi-rural area of Bhaktapur, Nepal. The program included two workshops covering aspects of poultry rearing including coop construction, chick rearing, biosecurity, and husbandry. Both workshops were a combination of lectures and hands-on learning. Following completion of the workshops, each farmer received subsidized materials for coop construction and poultry rearing. The co-operative provided training facilities and a market for selling eggs. Despite an outbreak of Highly Pathogenic Avian Influenza (HPAI), which affected the scale of program implementation, our results suggest that the workshop subsidy collaborative approach can be successful in reducing market entry barriers. Our 6-mo post-workshop survey showed that two-thirds of the workshop participants ultimately built their own coop and raised chicks. Half of these participants reported market available egg production and a doubling of egg consumption at home.

Augmentation of wild populations with captive-bred individuals presents an inherent risk of co-introducing novel pathogens to naive species, but it can be an important tool for supplementing small or declining populations. Game species used for human enterprise and recreation such as the ring-necked pheasant (Phasianus colchicus) are commonly raised in captivity and released onto public and private wildlands as a method of augmenting naturalized pheasant populations. This study presents findings on pathogen exposure from three sources of serological data collected in California during 2014-2017 including: (1) 71 pen-reared pheasants sampled across seven game bird breeding farms, (2) six previously released pen-reared pheasants captured at two study sites where wild pheasants occurred, and (3) 79 wild pheasants captured across six study sites. In both pen-reared and wild pheasants, antibodies were detected against hemorrhagic enteritis virus (HEV), infectious laryngotracheitis (ILT), infectious bursal disease virus (IBDV), paramyxovirus type 1 (PMV-1), and Pasteurella multocida (PM). Previously released pen-reared pheasants were seropositive for HEV, ILT, and PM. Generalized linear mixed models accounting for intra-class correlation within groups indicated that pen-reared pheasants were more than twice as likely to test positive for HEV antibodies. Necropsy and ancillary diagnostics were performed in addition to serological testing on 40 pen-reared pheasants sampled from five of the seven farms. Pheasants from three of these farms tested positive by PCR for Siadenovirus, the causative agent of both hemorrhagic enteritis in turkeys and marble spleen disease of pheasants, which are serologically indistinguishable. Following necropsy, owners from the five farms were surveyed regarding husbandry and biosecurity practices. Farms ranged in size from 10,000 to more than 100,000 birds, two farms raised other game bird species on premises, and two farms used some form of vaccination. Biosecurity practices varied by farm, but the largest farm implemented the strictest practices.

As social media becomes an ever-increasing staple of everyday life and a growing percentage of people turn to community driven platforms as a primary source of information, the data created from these posts can provide a new source of information from which to better understand an event in near real time. The 2018-2020 outbreak of Newcastle Disease (ND) in Southern California is the third outbreak of ND in Southern California within a 50-year time span. These outbreaks are thought to be primarily driven by non-commercial poultry (i.e. backyard and game fowl) in the region. Here we employed a commercial 'web crawling' tool between June of 2018 and July of 2020 which encompassed the majority of the outbreak in order to collect all available online mentions of 'virulent Newcastle Disease' (vND), the terminology commonly used by the California Department of Food and Agriculture (CDFA), United States Department of Agriculture (USDA), and the general public, in relation to the outbreak. A total of 2498 posts in English and Spanish were returned using a Boolean logic-based string search. While the number of posts was relatively small, their impact as measured by the number of visitors to the website and the number of people viewing the post (where provided) was much larger. Posts with negative sentiment were found to have a larger audience relative to posts with a positive sentiment. In addition, posts with negative sentiment peaked in May of 2019 which preceded the formation of the anti-depopulation group Save Our Birds (SOB). As the usage and impact of social media grows, the ability to utilize tools to analyze social media may improve both response and outreach-based strategies for various disease outbreaks including vND in Southern California which has a large non-commercial poultry population.

Migratory waterfowl are the primary reservoir of avian influenza viruses (AIV), which can be spread to commercial poultry. Surveillance efforts that track the location and abundance of wild waterfowl and link those data to inform assessments of risk and sampling for AIV currently do not exist. To assist surveillance and minimize poultry exposure to AIV, here we explored the utility of Remotely Sensed Moderate Resolution Imaging Spectroradiometer (MODIS) satellite imagery in combination with land-based climate measurements (e.g., temperature and precipitation) to predict waterfowl location and abundance in near real-time in the California Central Valley (CCV), where both wild waterfowl and domestic poultry are densely located. Specifically, remotely collected MODIS and climate data were integrated into a previously developed boosted regression tree (BRT) model to predict and visualize waterfowl distributions across the CCV. Daily model-based predictions are publicly available during the winter as part of the dynamic California Waterfowl Tracker (CWT) web app hosted on the University of California's Cooperative Extension webpage. In this study, we analyzed 52 days of model predictions and produced daily spatiotemporal maps of waterfowl concentrations near the 605 commercial poultry farms in the CCV during January and February of 2019. Exposure of each poultry farm to waterfowl during each day was classified as high, medium, low, or none, depending on the density of waterfowl within 4 km of a farm. Results indicated that farms were at substantially greater risk of exposure in January, when CCV waterfowl populations peak, than in February. For example, during January, 33% (199/605) of the farms were exposed for ≥1 day to high waterfowl densityLas aves acuáticas migratorias son el principal reservorio de los virus de la influenza aviar (con las siglas en inglés AIV), que pueden transmitirse a la avicultura comercial. Actualmente no existen esfuerzos de vigilancia que rastrean la ubicación y densidad de poblaciones de aves acuáticas silvestres y que vinculen esos datos para informar evaluaciones de riesgo y muestreo para influenza aviar. Para ayudar a la vigilancia y minimizar la exposición de la avicultura comercial a influenza aviar se exploró la utilidad de las imágenes satelitales por espectrorradiómetro de imágenes con resolución moderada (con las siglas en inglés MODIS) y de detección remota en combinación con mediciones climáticas terrestres (por ejemplo, temperatura y precipitación) para predecir la ubicación y densidad de aves acuáticas prácticamente en tiempo real en el Valle Central de California (CCV), donde tanto las aves acuáticas silvestres como las aves domésticas están densamente ubicadas. Específicamente, los datos MODIS y climáticos recopilados de forma remota se integraron en un modelo de árbol de regresión reforzado (BRT) desarrollado previamente para predecir y visualizar la distribución de las aves acuáticas en el Valle Central de California. Las predicciones diarias basadas en modelos están disponibles públicamente durante el invierno como parte de la aplicación dinámica en el del rastreador de aves acuáticas de California (California Waterfowl Tracker, CWT) ubicada en la página de internet de Extensión Cooperativa de la Universidad de California. En este estudio, se analizaron 52 días de predicciones del modelo y se produjeron mapas espaciotemporales diarios con densidades de aves acuáticas cerca de las 605 granjas avícolas comerciales en el Valle Central de California durante enero y febrero de 2019. La exposición de cada granja avícola a las aves acuáticas durante cada día se clasificó como alta, media, baja o nula, dependiendo de la densidad de aves acuáticas dentro de los cuatro kilómetros de una granja. Los resultados indicaron que las granjas tenían un riesgo sustancialmente mayor de exposición en enero, cuando las poblaciones de aves acuáticas en el Valle Central de California alcanzan su punto máximo, en comparación con febrero. Por ejemplo, durante enero, el 33% (199/605) de las granjas estuvieron expuestas durante más de un día a una alta densidad de aves acuáticas frente a un 19% (115/605) de las granjas en febrero. Además de demostrar la variabilidad general de la ubicación y densidad de las aves acuáticas, estos datos demuestran cómo se puede utilizar la teledetección para clasificar mejor los esfuerzos de bioseguridad y vigilancia para la influenza aviar mediante la utilización de una herramienta funcional basada en una aplicación en el internet. La capacidad de aprovechar la teledetección es un avance integral hacia la mejora de la vigilancia para influenza aviar en aves acuáticas en las proximidades de la avicultura comercial. La expansión de estos tipos de métodos de teledetección, vinculados a una herramienta en el internet que es fácil de usar, podría desarrollarse aún más en los Estados Unidos continentales. El modelo de árbol de regresión reforzado incorporado en el sistema de rastreo de aves acuáticas de California refleja un primer intento de brindar una representación precisa de la distribución y densidad de las aves acuáticas en relación con las aves comerciales.

As backyard poultry (BYP) ownership has increased in the US, the demand for veterinarians who treat BYP has also increased. However, veterinarians who treat BYP remain scarce and are mostly small animal veterinarians and exotic animal practitioners who have limited training in food animal regulatory practices. To gauge whether veterinary students are interested in learning more about BYP and what BYP topics to include in an online training program for veterinary students, a BYP knowledge assessment was conducted. Pre-clinical veterinary students were asked to self-rate their level of knowledge on various topics for both small animal practice and BYP using Likert-type ordinal scales. Wilcoxon signed-rank tests of those Likert data showed significant differences ( p < .01 at α = .05) between self-assessed knowledge of poultry and small animal medicine for all surveyed topics. Specifically, veterinary students ranked themselves as less knowledgeable on poultry concepts than on small animal medicine concepts. Nevertheless, students expressed interest in an online training program for treating BYP and drug residue avoidance in BYP, despite having chosen future career tracks that are not exclusively poultry. Specific topics students expressed interest in with respect to BYP training included anatomy, husbandry, prescribing medications, treatment options, food safety, antimicrobial resistance, and extra-label drug use.

SUMMARY The disposal of by-products, such as poultry litter, and carcasses is a serious issue because of risks associated with microbial pathogens, and controlling the pathogen risks requires identifying improved pre-treatment methods capable of inactivating pathogens. As poultry litter and carcasses are known to be major reservoirs of pathogenic microorganisms such as Salmonella and Escherichia coli (E. coli), improvement in existing understanding of the inactivation of these pathogens in poultry litter and carcasses is needed to determine the effective treatment time and temperature. Here we conducted a study to assess the thermal inactivation of 2 common bacteria in poultry productive systems: Escherichia coli (E. coli) and Salmonella enterica (Salmonella). The inactivation study was conducted at 50°C and 60°C using 3 different feedstocks: (1) poultry carcasses, (2) poultry litter, and (3) mixture of poultry litter and carcasses. Each feedstock was inoculated with known concentrations of E. coli and Salmonella prior to thermophilic digestion experiments at 50°C and 60°C. Regardless of feedstock types, E. coli survival was extended beyond 3 d at 50°C. In contrast, Salmonella was no longer detectable within 3 d at 50°C. At 60°C, both E. coli and Salmonella were undetected within an hour. There was no significant difference (at P

As commercial free-range and pastured poultry production has gained increased popularity in the United States in recent years, there is a greater need to understand basic husbandry practices including feeding and lighting practices. Because husbandry practices vary greatly between individual commercial pastured poultry and free-range operations, gaining knowledge across a wide cross-section of producers is necessary to better understand current practices. Specifically, because feed is considered the most expensive part of poultry production with respect to operating cost, in collaboration with the American Pastured Poultry Producers Association, an on-line survey of commercial free-range and pastured poultry producers was conducted aimed primarily at evaluating feeding and lighting practices. Data were collected from 14 commercial pastured (n = 13) and free-range (n = 1) producers (6 broiler, 1 layer, and 7 broiler/layer facilities) across 9 U.S. states. Results showed that these operations most commonly use Cornish Cross for broiler production and ISA Brown and Australorp for egg production. Only 1 of the 14 farms calculates feed conversion ratio on a monthly basis. Estimates of Hen Month Egg Production (HMEP) resulted in HMEP percentages that were over 100% in 6 of the 7 farms that provided data. 5 of the 7 farms that have layers used supplemental lighting but do not use a lux meter. These lack of data reflect an important challenge with this segment of the poultry industry. Extension based outreach focused on enabling data collection and record-keeping and analysis are necessary. Despite its small sample size, this study's results provide some valuable insights with respect to feeding equipment and the current state of data collection for this segment of the poultry industry.

Climate change will pose challenges for the world's food supply in the coming decades. As a leading agricultural state with a diverse agricultural portfolio, California will face its own unique regional challenges due to its complex agricultural inter-dependencies. As veterinarians and animal scientists with livestock and poultry clientele in the Central Valley of California, we are starting to observe changes in food safety, production efficiency, welfare and disease that can be linked to the effects of climate change. For example, in California drought has reduced access to rice hulls which are commonly used as bedding for poultry which have necessitated the use for recycling rice hulls. Our results have shown an 11.08 × greater risk ( P

Simple Summary An emerging threat to human and food animal health is the development of antimicrobial resistance in bacteria associated with food animals. One of the primary tools for assessing resistance levels and monitoring for changes in expressed resistance is the use of minimum inhibitory concentration tests, which expose bacterial isolates to a series of dilutions of an antimicrobial agent to identify the lowest concentration of the antimicrobial that effectively prevents bacterial growth. These tests produce a minimum inhibitory value that falls within a range of concentrations instead of an exact value, a process known as censoring. Analysis of censored data is complex and careful consideration of methods of analysis is necessary. The use of regression methods such as logistic regression that divide the data into two or three categories is relatively easy to implement but may not detect important changes in the distributions of data that occur within the categories. Models that do not simplify the data may be more complex but may detect potentially relevant changes missed when the data is categorized. As a result, the analysis of minimum inhibitory concentration data requires careful consideration to identify the appropriate model for the purpose of the study. Abstract The development of antimicrobial resistance (AMR) represents a significant threat to humans and food animals. The use of antimicrobials in human and veterinary medicine may select for resistant bacteria, resulting in increased levels of AMR in these populations. As the threat presented by AMR increases, it becomes critically important to find methods for effectively interpreting minimum inhibitory concentration (MIC) tests. Currently, a wide array of techniques for analyzing these data can be found in the literature, but few guidelines for choosing among them exist. Here, we examine several quantitative techniques for analyzing the results of MIC tests and discuss and summarize various ways to model MIC data. The goal of this review is to propose important considerations for appropriate model selection given the purpose and context of the study. Approaches reviewed include mixture models, logistic regression, cumulative logistic regression, and accelerated failure time–frailty models. Important considerations in model selection include the objective of the study (e.g., modeling MIC creep vs. clinical resistance), degree of censoring in the data (e.g., heavily left/right censored vs. primarily interval censored), and consistency of testing parameters (e.g., same range of concentrations tested for a given antibiotic).

Migratory waterfowl, including geese and ducks, are indicated as the primary reservoir of avian influenza viruses (AIv) which can be subsequently spread to commercial poultry. The US Department of Agriculture's (USDA) surveillance efforts of waterfowl for AIv have been largely discontinued in the contiguous United States. Consequently, the use of technologies to identify areas of high waterfowl density and detect the presence of AIv in habitat such as wetlands has become imperative. Here we identified two high waterfowl density areas in California using processed NEXt generation RADar (NEXRAD) and collected water samples to test the efficacy of two tangential flow ultrafiltration methods and two nucleic acid based AIv detection assays. Whole-segment amplification and long-read sequencing yielded more positive samples than standard M-segment qPCR methods (57.6% versus 3.0%, p&nbsp

Leveraging data collected by commercial poultry requires a deep understanding of the data that are collected. Machine learning (ML)-based techniques are capable of “learning by finding” nonobvious associations and patterns in the data in order to create more reliable, accurate, explanatory, and predictive statistical models. This article provides practical definitions and examples of ML-based statistical approaches for the analysis of poultry production and poultry food safety-based data. In addition to summarizing the literature, two real examples of the supervised machine learning ensemble technique, random forest (RF), are provided with respect to predicting egg weights from a commercial layer farm and identifying the potential causes of a Salmonella outbreak from a commercial broiler facility. Specifically, as an example, for the prediction of egg weights, a training model and a test model were created, and a modification of RF was used to explore the ability to predict egg weights. Results identified multiple variables including Age, Farm Location, Body Weight, Total Eggs, Hens Housed, and House Style which were predictive of the continuous variable Egg Weight. With respect to the accuracy of the variable Egg Weight, the average error between the predicted and actual egg weight was determined to be less than 3%. With respect to broiler food safety, a relational database was constructed and a supervised RF model was developed to identify the predictors of Salmonella in a grow-out farm and associated broiler processing plant. Predictors of Salmonella that included livability, density of birds in the grow-out farm, and breeder age were identified. The task of choosing the most appropriate ML-based model(s) that accounts for the large number of variables common to the poultry industry and addresses the intricate interdependence between several production parameters and inputs while predicting multiple sequential outputs is complex. The use of ML techniques in combination with new data streams including sensors (e.g., visual and audio), IoT, and Web-scraping could offer a more comprehensive, efficient, and timely approach toward evaluating productivity, food safety, and profitability in commercial poultry.

We investigated exposure to infectious diseases in wild (n=33) and pen-reared (n=12) Ring-necked Pheasants (Phasianus colchicus) in the Central Valley of California, US during 2014 and 2015. Serologic tests were positive for antibodies against hemorrhagic enteritis, infectious bursal disease, and Newcastle disease viruses in both wild and pen-reared pheasants.

In 2017, the Turlock branch of the California Animal HealthFood Safety laboratory system received a significant increase in infectious coryza (IC) necropsy cases, with a total of 54 submissions originating from commercial broilers (Caracterización de un brote de coriza infecciosa (

The application of RNA sequencing in commercial poultry could facilitate a novel approach toward food safety with respect to identifying conditions in food production that mitigate transcription of genes associated with virulence and survivability. In this study, we evaluated the effects of disinfectant exposure on the transcriptomes of two field isolates of Salmonella Heidelberg (SH) isolated from a commercial broiler processing plant in 1992 and 2014. The isolates were each exposed separately to the following disinfectants commonly used in poultry processing: cetylpyridinium chloride (CPC), acidified calcium hypochlorite (aCH), and peroxyacetic acid (PAA). Exposure times were 8 s with CPC to simulate a poultry processing dipping station or 90 min with aCH and PAA to simulate the chiller tank in a poultry processing plant at 4°C. Based on comparison with a publicly available annotated SH reference genome with 5,088 genes, 90 genes were identified as associated with virulence, pathogenicity, and resistance (VPR). Of these 90 VPR genes, 9 (10.0%), 28 (31.1%), and 1 (1.1%) gene were upregulated in SH 2014 and 21 (23.3%), 26 (28.9%), and 2 (2.2%) genes were upregulated in SH 2014 challenged with CPC, aCH, and PAA, respectively. This information and previously reported MICs for the three disinfectants with both SH isolates allow researchers to make more accurate recommendations regarding control methods of SH and public health considerations related to SH in food production facilities where SH has been isolated. For example, the MICs revealed that aCH is ineffective for SH inhibition at regulatory levels allowed for poultry processing and that aCH was ineffective for inhibiting SH growth and caused an upregulation of VPR genes.

Increases in global human population are leading to increasing demands for food production and waste management. Insect biomass is a sustainable alternative to traditional animal feeds when insects are produced on lignocellulosic by-products. Resources high in lignocellulose have high carbon to nitrogen ratios and require nitrogen supplementation to accelerate bioconversion. Here we report on studies that examine the influence of nitrogen supplementation of almond hull-based feedstocks on black soldier fly larvae (Hermetia illucens L.) cultivation and composition. Decreasing carbon to nitrogen ratio from 49 to 16 increased larvae harvest dry weight, specific larvae growth, and yield by 36%, 31%, and 51%, respectively. However, the decrease in carbon to nitrogen ratio decreased larvae methionine and cysteine contents by 11% and 13%, respectively. The findings demonstrate that carbon to nitrogen ratio can be managed to enhance bioconversion of lignocellulose to larvae, but that this management approach can reduce larvae amino acid content.

The increasing production of almonds worldwide has resulted in the significant generation of byproduct streams that require end uses. One potential use for byproducts is for cultivation of additional food sources including insects. Studies were performed to determine if black soldier fly larvae (Hermetia illucens L.) could be cultivated on almond byproducts (hulls and shells) and to examine the effect of aeration and moisture on larvae growth and hull composition.; Results: Increasing aeration from 0.04 to 0.36 mL min-1 g dry weight-1 tripled the harvest weight of larvae and increased larvae yield by a factor of five. Larvae calcium content increased by 18% with an increase in aeration from 0.04 to 0.95 mL min-1 g dry weight-1 . Moisture content also affected harvest dry weight and yield; increasing moisture content from 480 g kg-1 (wet basis) to 680 g kg-1 increased harvest weight by 56% and yield by a factor of 2. Variables did not affect larvae methionine and cysteine content. Low moisture content and aeration rate yielded an environment that supported microbial consumption of hulls over larvae consumption and growth.; Conclusions: The results demonstrate that almond hulls are a suitable feedstock for larvae production under controlled management of moisture content and aeration. © 2018 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.; © 2018 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

SUMMARY Riemerella anatipestifer infection accounts for the most significant economic losses due to infectious disease in commercial White Pekin ducks in the United States. An inactivated bacterin and a live attenuated vaccine are approved for use against R. anatipestifer in the United States. This study aimed to evaluate the duration of protection induced by the commercial bacterin containing formalin-inactivated strains of R. anatipestifer serotype 1, 2, 5 (RA1, RA2, RA5) combined with E. coli 078 (RA-EC). Pekin ducks were vaccinated twice at 2 and 3 wk of age with 0.5 mL of RA-EC bacterin containing approximately 108 colony forming units (CFU) of E. coli and 109 CFU of RA1, RA2 and RA5 per dose (0.5 mL). Four-, 6-, and 8-week-old vaccinated and non-vaccinated control ducks were subsequently challenged with virulent strains of either: E. coli 078, RA1, RA2 and RA5. Evaluation of the vaccine protective index, histopathology, and bacteriology indicate RA-EC bacterin provides protection against virulent stains of RA1, RA2, RA5, and E. coli O78 throughout the 8-wk commercial Pekin grow-out period.

Mitigation of Salmonella associated with poultry carcasses is primarily accomplished by rendering or carcass composting. While rendering temperatures and pressures are well established for pathogen inactivation in poultry carcasses, parameters controlling composting processes are less defined in part because multiple conditions and procedures are utilized. Consequently, limited knowledge exists describing the impacts of composting with varying temperature and mixing protocols with respect to the inactivation of Salmonella in poultry carcasses. To improve the existing knowledge of Salmonella survival in poultry carcasses, inactivation of Salmonella enterica serovar Typhimurium (ST) LT2 was investigated. The impacts of various composting temperatures (55, 62.5°C) and low-rendering (i.e., pasteurization) temperatures (70, 78°C) on Salmonella inactivation were tested in a bench-top setting using a ground carcass slurry and whole birds under mixed and non-mixed conditions. Results showed that the ground carcass slurry and the whole carcass exposed to temperatures consistent with composting had no detectable Salmonella after 110 h with a level of detection of one CFU/mL of ground carcass slurry and one CFU/g of whole carcasses, respectively. In addition, grinding of carcasses as opposed to whole carcasses was more predictable with respect to Salmonella heat inactivation. Furthermore, results showed that constant mixing decreased the overall time required to eliminate Salmonella under composting and low-rendering temperatures.

As pastured poultry production has gained increased popularity in the United States in recent years, there is a growing need for research and outreach efforts aimed at this sector of poultry production. In order to get familiarized with American pastured poultry producers, we conducted an online questionnaire aimed primarily at evaluating what operational challenges are faced by producers and what educational opportunities should be initiated by researchers. Results showed that pastured poultry farms largely vary in total number of acres farmed and total number of birds kept. The vast majority of farms (96%) rotate their flocks on pasture and include livestock species (78%) in their rotation systems. Mobile coops are the preferred housing option provided by producers (88%). The most common source of mortality listed by respondents was predation (52%), followed by "other" (32%). However, predation was not selected as the most important challenge by the majority of respondents. Sixty-four percent of participants instead mentioned providing adequate feed at reasonable cost as the major challenge in raising poultry on pasture, followed again by "other" (52%) and lack of processing facilities for small numbers of birds (40%). Finally, the topics considered by respondents as the most helpful to learn more about were how to improve egg production rate and/or feed conversion ratio (67%), followed by how to improve pasture condition and optimum vegetative cover all year round (62%). Despite its small sample size, this study's results provide some valuable insights of challenges encountered and information needed on pastured poultry farms.

Although infectious bronchitis virus (IBV) has been described as one of the most economically important viral respiratory diseases in poultry, there are few analyses of outbreaks that use spatial statistics. In order to better understand how the different genotypes of IBV behave spatially and temporally, we used geographic information system-based mapping coupled with spatial and spatial-temporal statistics to identify statistically significant clustering of multiple strains of infectious bronchitis (IB) between 2008 and 2012 in California. Specifically, space-time permutation and multinomial models were used to identify spatial and spatial-temporal clusters of various genotypes of IBV. Using time permutations (i.e., windows) spanning days to years, we identified three statistically significant ( P < 0.05) clusters. In contrast, multinomial models identified two statistically significant spatial-temporal clusters and one statistically significant spatial cluster. When comparing the space-time permutation and multinomial models against each other, we identified spatial and temporal overlap in two of the three statistically significant clusters. From a practical perspective, multinomial clustering approaches may be advantageous for studying IB because the model allows the different genotypes of IB to be independent nominal variables, thereby allowing for a more detailed spatial analysis. To that point, based on their risk ratios, the genotypes classified as vaccine-related were identified as the most significant contributor to two of the three mutinomial clusters. Additionally, statistically significant clusters were mapped and layered on a hot-spot analysis of commercial poultry farm density in order to qualitatively assess the relationship between farm density and clusters of IBV. Results showed that one of the three space-time permutations and one of the three multinomial clusters were spatially centered near the highest density farm areas, as determined by the hot-spot analysis.

In order to better understand collaboration among trainers in the backyard poultry community (i.e. feed store managers, youth development programs (i.e. 4-H), veterinarians, government agencies, extension resources and backyard poultry club leaders), Social Network Analysis (SNA) was used as a tool to better characterize and quantify the current collaboration network structure of backyard poultry trainers in California. Invited trainer attendees of two “Train-the-Trainers” poultry workshops (n = 67) held in Northern and Southern California were given a survey that asked them to list contacts that they collaborated with on backyard poultry (BYP) related work. The collaboration network in this study included a total of 109 trainers, 18 practitioners, and 32 individuals who are both trainers and practitioners for a total of 170 nodes (11 individuals did not have affiliation information available). In order to help identify central actors or collaboration leaders, the surveys were analyzed using Social Network Analysis (SNA), which allows for a quantitative analysis of relationships among various stakeholders. While the SNA showed that the existing collaboration network is disconnected with a clustering coefficient of 0.043 and median total degree centrality of 1 (range 9) and therefore not conducive for collaboration, key insights that could help restructure and improve the network were identified. As an example, among different poultry groups, 4-H was identified as the organization with the second highest median coverage score and fifth highest median centrality score. In addition, 4-H group leaders act as both trainers and practitioners. Consequently, outreach to 4-H group leaders throughout the state would potentially have the greatest impact with respect to overall coverage both inside and outside the 4-H network due to their high centrality and boundary spanning roles. Using SNA to strengthen the collaboration network infrastructure of backyard poultry trainers ultimately offers a more targeted approach toward extension for backyard poultry owners, which could ultimately facilitate communication and knowledge-sharing with BYP owners during a disease outbreak.

Raising backyard chickens is an ever-growing hobby in the United States. These flocks can be a substrate for respiratory disease amplification and transmission to commercial facilities. Five hundred fifty-four chickens from 41 backyard flocks were sampled in this study. ELISA kits were used to detect antibodies against avian influenza (AI), infectious laryngotracheitis (ILT), Newcastle disease (ND), infectious bronchitis (IB), Ornithobacterium rhinotracheale (ORT), Mycoplasma gallisepticum (MG), and Mycoplasma synoviae (MS). All visited flock owners answered a biosecurity questionnaire that assessed biosecurity measures. The questionnaire revealed that backyard poultry owners lack simple biosecurity measures such as use of dedicated shoes, their chicken sources are unreliable, and few of them benefit from veterinary oversight. Only one flock had a clear vaccination history against ND and IB. ORT, ND, IB, MS, MG, and ILT were the most seroprevalent in backyard poultry flocks with 97% (41/42), 77.5% (31/40), 75% (30/40), 73% (31/42), 69% (29/42), and 45% (19/42), respectively. The vaccinated flock was not considered in these calculations. When examining the distance between backyard flocks and the nearest commercial poultry facility, ND and MG were significantly more likely to be found in backyard flocks close to (4 miles) whereas ORT was significantly more likely in backyard chickens located far from (4 miles) commercial poultry. Birds purchased directly from National Poultry Improvement Plan hatcheries showed a reduced ND, MG, and MS antibody prevalence. Wearing dedicated shoes decreased MS antibody-positive birds. Finally, history of wild bird contact had a clear effect on an increased seroprevalence of NDV and MG. Serological results suggest that backyard poultry flocks have the potential to serve as a reservoir or amplifier for poultry respiratory diseases. The information generated in this project should direct extension efforts toward emphasizing the importance of small flock biosecurity and chick acquisition sources.

Very virulent infectious bursal disease virus (vvIBDv) was first detected in the United States at the end of 2008. Since its detection, Federal and State animal health officials, the poultry industry and the research/academic community have led response activities through a collaborative effort. By June 2011, much still remained unknown regarding the basic epidemiology and ecology of vvIBD in California, although there were a number of potential activities to fill this information gap. Available resources limited the ability to pursue all the activities, and responsible parties and stakeholders recognized the need to prioritize the activities. The analytic hierarchy process (AHP) is a useful multi-criteria decision making methodology that incorporates qualitative information (in the form of judgments) with available quantitative information. This is especially useful when there is very limited quantitative information, such as in the situation with vvIBD in California. A commercial package that allows ready use of the AHP model was utilized for prioritizing activities, incorporating input from members from the three stakeholder groups: State and Federal animal health officials, poultry industry, and research/academia. Based on their inputs on 17 potential activities, the participants identified three priority activities; specifically determination of risk factors for re-emergence or re-introduction at affected premises, development of a laboratory diagnostic test to screen for segment B of the vvIBDV genome and surveillance of other potential reservoirs (mealworms, rodents, beetles). In order to evaluate the ability of the AHP to respond to differences, a sensitivity analysis was done in order to evaluate changes in prioritization of activities. Changes in prioritization were noted demonstrating the plasticity of the model under different conditions. However, a 50% increase or decrease in weighting was necessary to affect the order of the three highest scoring activities. The use of a tool such as the AHP enables the development of a transparent, repeatable and flexible decision process, which can be useful in certain animal health response situations including the re-emergence of a previously eliminated disease or the introduction of a foreign animal disease.

In October of 2005 an outbreak of a vaccine-like strain of infectious laryngotracheitis (ILT), indistinguishable from the chicken embryo origin (CEO)-like vaccine strains, was detected by routine passive surveillance in the Central Valley of California, U. S. A. In response, a highly coordinated industry effort by two companies led to a significant decrease in the incidence of ILT over the same geographic region between 2008-2012. In order to understand the geographic and temporal spread of ILT in California before and after the outbreak, Global Information Systems (GIS) mapping coupled with spatial, temporal, and spatial- temporal statistics were used to identify retrospective and prospective low-rate clustering (i.e., less ILT than statistically expected) and high-rate clustering (i.e., more ILT than statistically expected) of ILT spatially and temporally. Results showed two high-rate retrospective spatial-temporal clusters and one low-rate prospective spatial-temporal cluster which were all statistically significant (P0.05). Overall, spatial-temporal clustering accounted for 36.9% of the positive ILT cases, while temporal clustering and spatial clustering done separately each accounted for 0% of the ILT cases, respectively. This demonstrates the utility of combining spatial and temporal clustering for ILT surveillance. Due to the risk of reversion to virulence and spread to immunologically naive broilers, future application of the CEO-based vaccine in the identified high rate spatial-temporal clusters should be avoided and other vaccine alternatives considered in order to avoid repeat outbreaks in those areas. This should especially be followed during the winter months of December, January, and February, which were found to have the highest prevalence of ILT (P0.05). Analysis of GIS data within the high-rate clusters showed that wind direction and farm density were minor factors in the spread of ILT. Shared roads may have played a role in the spread of ILT in one of the two high rate spatial-temporal clusters.

Poultry contaminated with Salmonella enterica subsp. enterica are a major cause of zoonotic foodborne gastroenteritis. Salmonella Heidelberg is a common serotype of Salmonella that has been implicated as a foodborne pathogen associated with the consumption of improperly prepared chicken. To better understand the effectiveness of common antimicrobial disinfectants (i.e., peroxyacetic acid [PAA], acidified hypochlorite [aCH], and cetylpyridinium chloride [CPC]), environmental isolates of nontyphoidal Salmonella were exposed to these agents under temperature, concentration, and contact time conditions consistent with poultry processing. Under simulated processing conditions (i.e., chiller tank and dipping stations), the bacteriostatic and bactericidal effects of each disinfectant were assessed against biofilm and planktonic cultures of each organism in a disinfectant challenge. Log reductions, planktonic MICs, and mean biofilm eradication concentrations were computed. The biofilms of each Salmonella isolate were more resistant to the disinfectants than were their planktonic counterparts. Although PAA was bacteriostatic and bactericidal against the biofilm and planktonic Salmonella isolates tested at concentrations up to 64 times the concentrations commonly used in a chiller tank during poultry processing, aCH was ineffective against the same isolates under identical conditions. At the simulated 8-s dipping station, CPC was bacteriostatic against all seven and bactericidal against six of the seven Salmonella isolates in their biofilm forms at concentrations within the regulatory range. These results indicate that at the current contact times and concentrations, aCH and PAA are not effective against these Salmonella isolates in their biofilm state. The use of CPC should be considered as a tool for controlling Salmonella biofilms in poultry processing environments.

Climate change will pose risks for the world’s food supply in the coming decades; this comes at a time when the global demand for food is expected to soar based on 2050 world population estimates. It is important to recognize that climate change will necessitate temporal and geographical shifts in food production, but will most likely not result in the collapse of our food systems. However, because of differences in the severity of how climate change will affect agriculture, regional and temporal changes in production and harvest-time will challenge the existing and sometimes outdated agricultural infrastructure with respect to collection, storage, transportation, and distribution of food. Increasing regional and global urbanization will further perturb these systems. Adaptation to climate change with respect to crop and food animal production will have to occur at multiple temporal, seasonal, and geospatial levels. Other major adaptation measures will have to occur with respect to crop selection, genetics, CO2 and temperature sensitivity, and resilience of crops and food animals, water resources, and mitigation of invasive species. Technology, including sophisticated Geographic Information Systems (GIS)-based modeling, coupled with publically available soil and weather data that help farmers optimize production and conservation will be essential toward adaptation. Communication of this type of localized technical information to agricultural stakeholders by national, federal, and state entities is beginning to occur in order to help farmers adapt and prepare for extreme events associated with climate change. As the largest agricultural state in the USA, California has developed a robust mitigation and adaptation strategy that may be useful for other nation-states.

Marek's disease (MD) is a major cause of mortality in backyard chickens. The diagnosis of MD is complex, however, and knowledge of Marek's disease virus (MDV) in spontaneous field cases such as in backyard chickens is largely unknown. In this study, 40 backyard chickens with a presumptive MD diagnosis based on histologic lymphoid infiltrations in peripheral nerves with and without lymphomas were investigated. Twenty-eight of the birds were submitted to the diagnostic laboratory for disease explorations, and 12 chickens were from a flock in which some members demonstrated anisocoria and pupil irregularities compatible with ocular MD. Histologic scores were established for brain, peripheral nerves, heart, lung, liver, kidney, and gonad sections, ranging from mild (+) to severe (+++) lymphoid infiltrations. Twelve chickens had gross lymphomas, and all but two chickens had mild to severe peripheral nerve lymphoid infiltrates. There were no age or breed predispositions in the study group. Quantification of serotypes MDV-1, -2, and -3 performed with real-time PCR demonstrated high correlation (R

Foodborne pathogens such as Salmonella that survive cleaning and disinfection during poultry processing are a public health concern because pathogens that survive disinfectants have greater potential to exhibit resistance to antibiotics and disinfectants after their initial disinfectant challenge. While the mechanisms conferring antimicrobial resistance (AMR) after exposure to disinfectants is complex, understanding the effects of disinfectants on Salmonella in both their planktonic and biofilm states is becoming increasingly important, as AMR and disinfectant tolerant bacteria are becoming more prevalent in the food chain. This review examines the modes of action of various types of disinfectants commonly used during poultry processing (quaternary ammonium, organic acids, chlorine, alkaline detergents) and the mechanisms that may confer tolerance to disinfectants and cross-protection to antibiotics. The goal of this review article is to characterize the AMR profiles of Salmonella in both their planktonic and biofilm state that have been challenged with hexadecylpyridinium chloride (HDP), peracetic acid (PAA), sodium hypochlorite (SHY) and trisodium phosphate (TSP) in order to understand the risk of these disinfectants inducing AMR in surviving bacteria that may enter the food chain.

In 2017, the Turlock branch of the California Animal Health & Food Safety laboratory system received a significant increase in infectious coryza (IC) necropsy cases, with a total of 54 submissions originating from commercial broilers (n = 40), commercial layers (n = 11), and backyard chickens (n = 3). Layer flocks positive for IC were distributed within the adjacent counties of Merced and Stanislaus, while broiler flocks were concentrated within Merced County. The backyard flocks were located in Alameda and Sacramento counties. The clinical and pathologic presentation was consistent with IC, although septicemic lesions were also noticed. Avibacterium paragallinarum was isolated and identified by PCR from the respiratory tract as well as from extrarespiratory sites. Polymicrobial infections involving other viral (infectious bronchitis virus, infectious bursal disease virus) and bacterial (Mycoplasma spp., Escherichia coli, Ornithobacterium rhinotracheale, Gallibacterium anatis biovar haemolytica) agents were commonly reported. Thirteen selected Av. paragallinarum isolates were successfully characterized as serovar C (Page scheme) and serovar C2 (Kume scheme). They shared a unique enterobacterial repetitive intergenic consensus (ERIC) PCR, differing from the four reference strains, and showed consistent high minimum inhibitory concentration values for tetracycline, suggesting a common origin from a single clone. Based on these results, high biosecurity standards and proper immunization of susceptible, multi-age flocks should always be implemented and adjusted as needed. The importance of backyard flocks should not be underestimated due to their unique epidemiologic role.

Between July 2007 and December 2011, 2660 environmental drag swab samples were collected in total from California layer flocks on behalf of the California Egg Quality Assurance Program (CEQAP), the egg safety rule (21 CFR Parts 16 and 118) of the Food and Drug Administration (FDA), or both. The samples were processed by the California Animal Health and Food Safety Lab, and positive or negative results for Salmonella enterica serovar Enteritidis (SE) were recorded. This study retrospectively compares the differences between the FDA and CEQAP programs with respect to their SE environmental sampling surveillance results. To accomplish this comparison, two different CEQAP (new and old) data sets representing different SE environmental surveillance approaches in the life of the flock were compared against each other and against the FDA's SE environmental testing plan. Significant differences were noted between the CEQAP and FDA programs with respect to the prevalence of SE in the farm environment. Analyses of the prevalence of SE at different stages in the flock's life cycle (chick papers, preproduction, midproduction, postmolt, and premarket) found the highest prevalence of SE in premarket (11.9%), followed by postmolt (3.5%) and midproduction (3.4%), and there was a tie between chick papers and preproduction (2.1%). To assess the main effects of the presence of SE in the farm environment, backwards binary logistic regression was used. Of six independent variables examined (age of flock, year, season, owner, CEQAP membership, and analysis of pooled samples vs. individual swabs), only age of flock, owner, and year were determined to be significant factors in the final model. Although CEQAP membership and pooling vs. individuals swabs were not included in the final model, Pearson chi-square tests did show significantly higher odds of SE for non-CEQAP member farms and higher odds of SE in pooled samples vs. individual swabs.

To better understand the potential avian diseases in Greater Sage-grouse (Centrocercus urophasianus) in the Great Basin in Nevada, US, we collected 31 blood samples March–April 2014 and tested for antibodies to eight viruses and two bacteria. Specifically, sera were tested for antibodies to avian leukosis virus type A, B, and J (ALV-A, ALV-B, and ALV-J, respectively), infectious bursal disease virus, infectious bronchitis virus, reticuloendothelial virus, avian influenza virus (AIV), West Nile virus, Pasteurella multocida (PM), and Salmonella enterica serovar Pullorum. Serum antibodies against ALV-A and -B (1/31, 3%), ALV-J (5/31, 16%), PM (1/31, 3%), and AIV (2/31, 6%) were detected by enzyme-linked immunosorbent assay (ELISA). While ELISA tests used have only been validated in domestic poultry, the serologic data should be used as a potential indicator of the range of bacterial and viral infectious agents that can infect the Greater Sage-grouse.

On the basis of the data from the California Animal Health and Food Safety Laboratory System, 1444 infectious bronchitis (IB) cases were diagnosed between 1997 and 2012. Epidemiologic analyses demonstrated two major IB virus (IBV) outbreak peaks, affecting mainly 35-to-49-day-old broiler chickens. California variant 1737 (CA1737) and California variant 1999 (Cal 99) IBV types were the most prevalent genotypes during the analyzed period. To further understand the increased prevalence of these genotypes, we assessed and compared the variability of the S1 gene hypervariable region of CA1737 and Cal 99 with the variability of IBV strains belonging to the Massachusetts 41 (M41) and Arkansas (Ark) types during serial passages in embryonated chicken eggs. On the basis of the S1 nonsynonymous changes, seven different subpopulations were detected in M41. However, the predominant population of the field strain M41 before passages continued to be predominant throughout the experiment. In contrast, Ark passaging resulted in the detection of 13 different subpopulations, and the field sequence became extinct after the first passage. In IBV Cal 99, eight different subpopulations were detected; one of these became predominant after the second passage. In CA1737, 10 different subpopulations were detected. The field strain major sequence was not detected after the first passage but reappeared after the second passage and remained at low levels throughout the experiment. Compared with M41 and Ark, Cal 99 and CA1737 showed intermediate variability.

While pasture-raised poultry comprises a small portion of the commercial poultry industry in North America, these alternative rearing systems have become increasingly popular. As such, it is critical to improve our understanding of husbandry practices and prevalence of zoonotic and epizoonotic diseases in these systems. This research reviews the results of a survey sent to 82 commercial pastured poultry farms in California. While the survey response was low (13.4%), it was enhanced by detailed in-person interviews and farm visits. In addition, we conducted drag swabs for Salmonella Enteritidis. On average, farms utilized 12.3% of their total farmland for pastured poultry operations, which often coexisted with other livestock (45%), touch crops (27%), and non-touch crops (45%). While the mean (44.6 sq. ft./hen) and median (22.2 sq. ft./hen) pasture stocking densities were within auditing guidelines, the mean (1.2 sq. ft./hen) and median (0.5 sq. ft./hen) coop stocking densities were below the pending USDA (2016) guidelines recommended in 7 CFR Part 205. Drag swab results showed the presence of Salmonella Enteritidis (SE) in the environment of one of the 11 farms (9.1%). In addition, Salmonella Pullorum (SP) whole blood agglutination tests were used to understand the prevalence of Salmonella spp. in laying hens within the studied farms. Results showed the presence of antibodies in flocks at six of the seven non-SE vaccinated farms, with a mean on-farm prevalence of 25.6% in laying hens. Logistic regression was used to determine risk factors for Group D Salmonella exposure in non-vaccinated flocks, using the SP blood agglutination data as the dependent variable and the survey questions as the independent variables. Statistically significant (P

Single swabs (cultured individually) are currently used in the Food and Drug Administration (FDA) official method for sampling the environment of commercial laying hens for the detection of Salmonella enterica ssp. serovar Enteritidis (Salmonella Enteritidis). The FDA has also granted provisional acceptance of the National Poultry Improvement Plan's (NPIP) Salmonella isolation and identification methodology for samples taken from table-egg layer flock environments. The NPIP method, as with the FDA method, requires single-swab culturing for the environmental sampling of laying houses for Salmonella Enteritidis. The FDA culture protocol requires a multistep culture enrichment broth, and it is more labor intensive than the NPIP culture protocol, which requires a single enrichment broth. The main objective of this study was to compare the FDA single-swab culturing protocol with that of the NPIP culturing protocol but using a four-swab pool scheme. Single and multi-laboratory testing of replicate manure drag swab sets (n = 525 and 672, respectively) collected from a Salmonella Enteritidis-free commercial poultry flock was performed by artificially contaminating swabs with either Salmonella Enteritidis phage type 4, 8, or 13a at one of two inoculation levels: low, x¯ = 2.5 CFU (range 2.5-2.7), or medium, x¯ = 10.0 CFU (range 7.5-12). For each replicate, a single swab (inoculated), sets of two swabs (one inoculated and one uninoculated), and sets of four swabs (one inoculated and three uninoculated), testing was conducted using the FDA or NPIP culture method. For swabs inoculated with phage type 8, the NPIP method was more efficient (P0.05) for all swab sets at both inoculation levels than the reference method. The single swabs in the NPIP method were significantly (P0.05) better than four-pool swabs in detecting Salmonella Enteritidis at the lower inoculation level. In the collaborative study (n = 13 labs) using Salmonella Enteritidis phage type 13a inoculated swabs, there was no significant difference (P0.05) between the FDA method (single swabs) and the pooled NPIP method (four-pool swabs). The study concludes that the pooled NPIP method is not significantly different from the FDA method for the detection of Salmonella Enteritidis in drag swabs in commercial poultry laying houses. Consequently based on the FDA's Salmonella Enteritidis rule for equivalency of different methods, the pooled NPIP method should be considered equivalent. Furthermore, the pooled NPIP method was more efficient and cost effective.

Bioaerosol Mass Spectrometry (BAMS), a real-time single cell analytical technique, was used to follow the biochemical and morphological changes within a group of Bacillus atrophaeus cells by measuring individual cells during the process of sporulation. A mutant of B. atrophaeus that lacks the ability to produce dipicolinic acid (DPA) was also analyzed. Single cell aerodynamic sizing was used to follow gross morphological changes, and chemical analysis of single cells by mass spectrometry was used to follow some biochemical changes of B. atrophaeus cells during endospore formation.

Single-particle laser desorption/ionization time-of-flight mass spectrometry, in the form of bioaerosol mass spectrometry (BAMS), was evaluated as a rapid detector for individual airborne, micron-sized, Mycobacterium tuberculosis H37Ra particles, comprised of a single cell or a small number of clumped cells. The BAMS mass spectral signatures for aerosolized M. tuberculosis H37Ra particles were found to be distinct from M. smegmatis , Bacillus atrophaeus , and B. cereus particles, using a distinct biomarker. This is the first time a potentially unique biomarker was measured in M. tuberculosis H37Ra on a single-cell level. In addition, M. tuberculosis H37Ra and M. smegmatis were aerosolized into a bioaerosol chamber and were sampled and analyzed using BAMS, an aerodynamic particle sizer, a viable Anderson six-stage sampler, and filter cassette samplers that permitted direct counts of cells. In a background-free environment, BAMS was able to sample and detect M. tuberculosis H37Ra at airborne concentrations of >1 M. tuberculosis H37Ra-containing particles/liter of air in 20 min as determined by direct counts of filter cassette-sampled particles, and concentrations of >40 M. tuberculosis H37Ra CFU/liter of air in 1 min as determined by using viable Andersen six-stage samplers. This is a first step toward the development of a rapid, stand-alone airborne M. tuberculosis particle detector for the direct detection of M. tuberculosis bioaerosols generated by an infectious patient. Additional instrumental development is currently under way to make BAMS useful in realistic environmental and respiratory particle backgrounds expected in tuberculosis diagnostic scenarios.

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers approximately 99% of the euchromatic genome and is accurate to an error rate of approximately 1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human genome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.

Liquid array-based multiplexed immunoassays designed for rapid, sensitive, specific, and simultaneous detection of multiple simulants of biological warfare agents have been developed. In both blind and standard laboratory trials, we demonstrate the simultaneous detection of four simulant agents from a single sample. The challenge agents comprise broad classes of pathogens (virus, protein toxins, bacterial spores, vegetative cells). Assay performance of each analyte was optimized, and dose-response curves and the limits of detection (LODs) for individual analytes are presented. Assay performance, including dynamic range, sensitivity, and LODs for liquid arrays and enzyme-linked immunosorbant assay were compared and are shown to be similar. Maximum assay sensitivity is obtained in approximately 1 h, and good sensitivity is achieved in as little as 30 min. Although the sample matrixes are very complex, even for highly multiplexed assays the samples do not exhibit evidence of nonspecific binding, demonstrating that the assays also have high specificity.

Although it has become increasingly popular to keep backyard chickens in the United States, few studies have provided information about these flocks. An online survey of backyard chicken owners was conducted, advertised through Master Gardeners' websites, social platforms, and other sites. The survey had 56 questions about flock history, husbandry, health care, and owner attitudes and demographics. Surveys received (n = 1,487) came almost equally from urban, suburban, and rural areas. Most (71%) respondents owned fewer than 10 chickens and had kept chickens for less than 5 yr (70%). Major reasons for keeping chickens were as food for home use (95%), gardening partners (63%), pets (57%), or a combination of these. Rural respondents had larger flocks (P ≤ 0.001) and were more likely to keep chickens as a source of income or for show (P ≤ 0.001) than urban and suburban respondents. Owners thought that eggs/meat from their chickens were more nutritious (86%), safer to consume (84%), and tasted better (95%) than store-bought products, and also that the health and welfare of their chickens was better (95%) than on commercial farms. The majority (59%) indicated no flock health problems in the last 12 mo. However, there was a lack of awareness about some poultry health conditions. Many knew either little or nothing about exotic Newcastle or Marek's disease, and most (61%) did not vaccinate against Marek's. Respondents wanted to learn more about various flock management topics, especially how to detect (64%) and treat (66%) health problems. The Internet was the main source of information (87%) used by backyard flock owners, followed by books/magazines (62%) and feed stores (40%). Minimizing predation was the most cited challenge (49%), followed by providing adequate feed at low cost (28%), dealing with soil management (25%), and complying with zoning regulations (23%). The evidence obtained from this survey will help to determine what information and resources are needed to maintain good biosecurity and improve the health and welfare of backyard flocks.

In December of 2008 very virulent infectious bursal disease virus (vvIBDV) was identified in a commercial flock in northern California. Since then several other backyard and commercial facilities in California have had flocks affected by the same strain and other unique (previously unseen) strains of IBDV. Previous to this incident, very virulent infectious bursal disease (vvIBD) had never been identified in North America. Following the initial outbreak in 2008, California became the first state to undertake a voluntary surveillance effort to try to determine the geographical prevalence of vvIBD based on sequencing of a portion of the segment A region of the vvIBDV genome. To date we have complete geographical information on approximately 500 separate accessions representing approximately 1500 birds from over 200 commercial (-85% of the facilities) and backyard facilities (-15% of the facilities) throughout the state. Sequencing of targeted regions of both the segment A and segment B regions of the genome has revealed three distinct types of IBDV in California chickens. One type is genetically and in pathogenically consistent with vvIBDV. The second and third types only have a segment A region consistent with vvIBDV. Geographic information system mapping coupled with spatial-temporal cluster analysis identified significant spatial and time-space clustering; however, no temporal clustering was noted. The lack of temporal clustering coupled with negative vvIBDV results in tested avian wildlife implies that avian wildlife in California do not currently appear to play a significant role in vvIBDV transmission. In the voluntary surveillance that was done in the Central Valley of California, which has a high density of commercial poultry, no positive farms were found when 142 of 504 farms were sampled. Given this level of sampling, the confidence (probability) of detecting an affected commercial flock was calculated to be between 28% and 81% depending on whether one or five hypothetically affected farms were affected.

The United Nations, Food and Agricultural Organization [ FAO, Steinfeld, Gerber, Wassenaar, Castel, Rosales, and de Haan (2006) . Livestock's Long Shadow. Food and Agriculture Organization of the United Nations] report titled Livestock's Long Shadow (LLS) stated that 18% (approximately 7100 Tg CO 2 -eq yr − 1 ) of anthropogenic greenhouse gases (GHGs) are directly and indirectly related to the world's livestock. The report's statement that livestock production is responsible for a greater proportion of anthropogenic emissions than the entire global transportation sector (which emits 4000–5200 Tg CO 2 -eq yr − 1 ) is frequently quoted in the public press [ Fox News and Kroll (2009) . A Tearful, Reluctant Farewell to My Favorite Food: Meat; LA Times (2007) . A warming world; pollution on the hoof; livestock emissions are a leading source of greenhouse gases. One solution may be to eat less meat, Los Angeles; NY Times, Op-ed. (2009) . Meat and the Planet. New York City] and continues to inform public policy. Recent estimates by the United States Environmental Protection Agency [ EPA, Hockstad, Weitz (2009) . Inventory of U.S. greenhouse gases and sinks: 1990–2007. Environmental Protection Agency] and the California Energy Commission [ CEC—California Energy Commission (2005) . Inventory of California Greenhouse Gas Emissions and Sinks: 1990 to 2002 Update] on the impacts of livestock on climate change in the United States and California have arrived at much different GHG estimates associated with direct livestock emissions (enteric fermentation and manure), totaling at less than 3% of total anthropogenic GHG and much smaller indirect emissions compared to the global assessment. Part of the difference of the global versus national predictions is due to the significant weight that has been assigned to the category of “land-use change” patterns related to livestock production (mainly deforestation). Furthermore, LLS attempts a life cycle assessment for global livestock production but does not use an equally holistic approach for its transportation prediction numbers. The primary focus of the present paper is to examine the relative contributions of livestock to climate change at different geographical and production scales. [ Note : CO 2 equivalents (CO 2 -eq.) represent the total impact (radiative forcing) of GHG in the atmosphere, thereby making it possible to determine the climate change impact of one GHG versus another EPA [ EPA and Holtkamp, Irvine, John, Munds-Dry, Newland, Snodgrass, and Williams (2006) . “Inventory of U.S. Green House Gases and Sinks: 1996–2006.”]. The definition of the Global Warming Potential (GWP) for a particular GHG is the ratio of heat trapped by one unit mass of the GHG to that of one unit mass of CO 2 (the GWP of CO 2 is one) over a specific period of time [IPCC (2001). IPCC Third Assessment Climate Change 2001. A Report of the Intergovernmental Panel on Climate Change]. The 100-year GWP for CH 4 and N 2 O are 23 times and 296 times the GWP of CO 2 , respectively [IPCC (2001). IPCC Third Assessment Climate Change 2001. A Report of the Intergovernmental Panel on Climate Change]. Therefore, for simplicity sake it is common practice to combine the total effects of CO 2 , CH 4 , and N 2 O into CO 2 equivalents (or CO 2 -eq).]