Phenotypic and genotypic characterization of antimicrobial resistance of non-typhoidal Salmonella from retail meat in California.

Antimicrobial resistance (AMR) is a global emerging problem for food safety and public health. Retail meat is one of the vehicles that may transmit antimicrobial resistant bacteria to humans. Here we assessed the phenotypic and genotypic resistance of non-typhoidal Salmonella from retail meat collected in California in 2019 by the National Antimicrobial Resistance Monitoring System (NARMS) Retail Food Surveillance program. A total of 849 fresh meat samples were collected from randomly selected grocery stores in Northern and Southern California from January to December 2019. The overall prevalence of Salmonella was 15.31 %, with a significantly higher occurrence in Southern (28.38%) than in Northern (5.22 %) California. The prevalence of Salmonella in chicken (24.01 %) was higher (p < 0.001) compared to ground turkey (5.42 %) and pork (3.08 %) samples. No Salmonella were recovered from ground beef samples. The prevalence of Salmonella in meat with reduced antibiotic claim (20.35 %) was higher (p < 0.001) than that with conventional production (11.96 %). Salmonella isolates were classified into 25 serotypes with S. Kentucky (47.73 %), S. typhimurium (11.36 %), and S. Alachua (7.58 %) as predominant serotypes. Thirty-two out of 132 (24.24 %) Salmonella isolates were susceptible to all tested antimicrobial drugs, while 75.76 % were resistant to one or more drugs, 62.88 % to two or more drugs, and 9.85 % to three or more drugs. Antimicrobials that Salmonella exhibited high resistance to were tetracycline (82/132, 62.12 %) and streptomycin (79/132, 59.85 %). No significant difference was observed between reduced antibiotic claim and conventional production in the occurrence of single and multidrug resistance. A total of 23 resistant genes, a D87Y mutation of gyrA, and 23 plasmid replicons were identified from resistant Salmonella isolates. Genotypic and phenotypic results were well correlated with an overall sensitivity of 96.85 %. S. infantis was the most resistant serotype which also harbored the IncFIB (pN55391) plasmid replicon and gyrA (87) mutation. Data from Northern and Southern California in this study helps us to understand the AMR trends in Salmonella from retail meat sold in the highly populous and demographically diverse state of California.

Assessment of Prevalence and Diversity of Antimicrobial Resistant Escherichia coli from Retail Meats in Southern California.

Retail meat products may serve as reservoirs and conduits for antimicrobial resistance, which is frequently monitored using Escherichia coli as indicator bacteria. In this study, E. coli isolation was conducted on 221 retail meat samples (56 chicken, 54 ground turkey, 55 ground beef, and 56 pork chops) collected over a one-year period from grocery stores in southern California. The overall prevalence of E. coli in retail meat samples was 47.51% (105/221), with E. coli contamination found to be significantly associated with meat type and season of sampling. From antimicrobial susceptibility testing, 51 isolates (48.57%) were susceptible to all antimicrobials tested, 54 (51.34%) were resistant to at least 1 drug, 39 (37.14%) to 2 or more drugs, and 21 (20.00%) to 3 or more drugs. Resistance to ampicillin, gentamicin, streptomycin, and tetracycline were significantly associated with meat type, with poultry counterparts (chicken or ground turkey) exhibiting higher odds for resistance to these drugs compared to non-poultry meats (beef and pork). From the 52 E. coli isolates selected to undergo whole-genome sequencing (WGS), 27 antimicrobial resistance genes (ARGs) were identified and predicted phenotypic AMR profiles with an overall sensitivity and specificity of 93.33% and 99.84%, respectively. Clustering assessment and co-occurrence networks revealed that the genomic AMR determinants of E. coli from retail meat were highly heterogeneous, with a sparsity of shared gene networks.

Analyzing public sentiment toward GMOs via social media between 2019-2021.

Genetically modified organisms or GMOs offer significant advantages in food production, including increased yield, decreased pesticide usage, and better disease resistance. However, adoption and public sentiment toward GMOs is highly variable. Without positive sentiment toward GMOs, consumption of GMO-based foods may not have an adequate market for further investment. In order to better understand overall public sentiment toward GMO-based foods, a Boolean search was created using a commercial web-crawling service to collect and analyze public sentiment of GMOs across multiple social media and web-based services from May 1, 2019, to May 31, 2021. The Boolean query identified 2 million mentions of GMOs during the study period. Using the commercial software's sentiment analysis (i.e. classifying mentions as either neutral, negative, or positive), 54% of the mentions were categorized as having a neutral sentiment, 32% as having a negative sentiment, and 14% as having a positive sentiment. Further emotional analysis (classifying posts by the emotion expressed, e.g., disgust, joy, sadness, anger, fear, surprise) produced by the software shows that the majority of the mentions were categorized as expressing a negative emotion: 31% of mentions expressed disgust, 28% joy, 18% sadness, 16% anger, 7% fear, and 1% surprise. Among the various social media sources collected, Twitter was the main source of data, providing 62% of the total 2 million mentions, followed by 14% from news sources and 12% from Reddit. These types of data can be used to better understand trends in sentiment toward GMOs and ultimately play an important role in combating mis-information.

Assessing a pilot co-operative-based workshop-subsidy model toward improving small-scale chicken production in peri-urban Nepal.

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.

Antimicrobial Resistance Profiles of Non-typhoidal Salmonella From Retail Meat Products in California, 2018.

Non-typhoidal Salmonella remains a leading cause of foodborne illness in the United States, with food animal products serving as a key conduit for transmission. The emergence of antimicrobial resistance (AMR) poses an additional public health concern warranting better understanding of its epidemiology. In this study, 958 retail meat samples collected from January to December 2018 in California were tested for Salmonella. From multivariable logistic regression, there was a 6.47 (90% CI 2.29-18.27), 3.81 (90% CI 1.29-11.27), and 3.12 (90% CI 1.03-9.45) higher odds of contamination in samples purchased in the fall, spring, and summer than in winter months, respectively, and a 3.70 (90% CI 1.05-13.07) higher odds in ground turkey compared to pork samples. Fourteen distinct serotypes and 17 multilocus sequence types were identified among the 43 isolates recovered, with S. Kentucky (25.58%), S. Reading (18.60%), S. Infantis (11.63%), and S. Typhimurium (9.30%) comprising the top serotypes. High prevalence of resistance was observed in retail chicken isolates for streptomycin (12/23, 52.17%) and tetracycline (12/23, 52.17%), in ground turkey isolates for ampicillin (8/15, 53.34%), and in ground beef isolates for nalidixic acid (2/3, 66.67%). Fourteen (32.56%) were susceptible to all antimicrobials tested, 11 (25.58%) were resistant to one drug, and 12 (27.91%) were resistant to two drugs. The remaining six isolates (13.95%) were multidrug-resistant (MDR, ≥3 drug classes) S. Infantis (n = 4), S. Reading (n = 1), and S. Kentucky (n = 1). Whole-genome sequencing (WGS) identified 16 AMR genes and 17 plasmid replicons, including bla CTX-M-65 encoding ceftriaxone resistance and a D87Y mutation in gyrA conferring resistance to nalidixic acid and reduced susceptibility to ciprofloxacin. The IncFIB(pN55391) replicon previously identified in connection to the worldwide dissemination of pESI-like mega plasmid carriage in an emerged S. Infantis clone was detected in four of the six MDR isolates. Genotypes from WGS showed high concordance with phenotype with overall sensitivity and specificity of 95.31% and 100%, respectively. This study provides insight into the AMR profiles of a diversity of Salmonella serotypes isolated from retail meat products in California and highlights the value of routine retail food surveillance for the detection and characterization of AMR in foodborne pathogens.

Pathways for avian influenza virus spread: GPS reveals wild waterfowl in commercial livestock facilities and connectivity with the natural wetland landscape.

Zoonotic diseases are of considerable concern to the human population and viruses such as avian influenza (AIV) threaten food security, wildlife conservation and human health. Wild waterfowl and the natural wetlands they use are known AIV reservoirs, with birds capable of virus transmission to domestic poultry populations. While infection risk models have linked migration routes and AIV outbreaks, there is a limited understanding of wild waterfowl presence on commercial livestock facilities, and movement patterns linked to natural wetlands. We documented 11 wild waterfowl (three Anatidae species) in or near eight commercial livestock facilities in Washington and California with GPS telemetry data. Wild ducks used dairy and beef cattle feed lots and facility retention ponds during both day and night suggesting use for roosting and foraging. Two individuals (single locations) were observed inside poultry facility boundaries while using nearby wetlands. Ducks demonstrated high site fidelity, returning to the same areas of habitats (at livestock facilities and nearby wetlands), across months or years, showed strong connectivity with surrounding wetlands, and arrived from wetlands up to 1251 km away in the week prior. Telemetry data provides substantial advantages over observational data, allowing assessment of individual movement behaviour and wetland connectivity that has significant implications for outbreak management. Telemetry improves our understanding of risk factors for waterfowl-livestock virus transmission and helps identify factors associated with coincident space use at the wild waterfowl-domestic livestock interface. Our research suggests that even relatively small or isolated natural and artificial water or food sources in/near facilities increases the likelihood of attracting waterfowl, which has important consequences for managers attempting to minimize or prevent AIV outbreaks. Use and interpretation of telemetry data, especially in near-real-time, could provide key information for reducing virus transmission risk between waterfowl and livestock, improving protective barriers between wild and domestic species, and abating outbreaks.

Web crawling of social media and related web platforms to analyze backyard poultry owners responses to the 2018-2020 Newcastle Disease (ND) outbreak in Southern California.

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.

Health surveillance of a potential bridge host: Pathogen exposure risks posed to avian populations augmented with captive-bred pheasants.

Augmentation of wild populations with captive-bred individuals presents an inherent risk of co-introducing novel pathogens to naïve 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 (a) 71 pen-reared pheasants sampled across seven game bird breeding farms, (b) six previously released pen-reared pheasants captured at two study sites where wild pheasants occurred and (c) 79 wild pheasants captured across six study sites. In both pen-reared and wild pheasants, antibodies were detected against haemorrhagic 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 intraclass 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 haemorrhagic 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.

Assessing Backyard Poultry versus Small Animal Knowledge of Veterinary Students regarding Husbandry, Prescription Drug Use, and Antimicrobial Resistance.

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.

Using the California Waterfowl Tracker to Assess Proximity of Waterfowl to Commercial Poultry in the Central Valley of California.

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 density vs. 19% (115/605) of the farms in February. In addition to demonstrating the overall variability of waterfowl location and density, these data demonstrate how remote sensing can be used to better triage AIV surveillance and biosecurity efforts via the utilization of a functional web app-based tool. The ability to leverage remote sensing is an integral advancement toward improving AIV surveillance in waterfowl in close proximity to commercial poultry. Expansion of these types of remote sensing methods, linked to a user-friendly web tool, could be further developed across the continental United States. The BRT model incorporated into the CWT reflects a first attempt to give an accurate representation of waterfowl distribution and density relative to commercial poultry.

Las 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.

A comparison of amplification methods to detect Avian Influenza viruses in California wetlands targeted via remote sensing of waterfowl.

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 < .0001). We determined that this difference in positivity was due to mismatches in published primers to our samples and that these mismatches would result in failing to detect in the vast majority of currently sequenced AIv genomes in public databases. The whole segment sequences were subsequently used to provide subtype and potential host information of the AIv environmental reservoir. There was no statistically significant difference in sequencing reads recovered from the RexeedTM filtration compared to the unfiltered surface water. This overall approach combining remote sensing, filtration and sequencing provides a novel and potentially more effective, surveillance approach for AIv.

Overview of Quantitative Methodologies to Understand Antimicrobial Resistance via Minimum Inhibitory Concentration.

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).

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.

Managing high fiber food waste for the cultivation of black soldier fly larvae.

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.

Understanding Antimicrobial Resistance (AMR) Profiles of Salmonella Biofilm and Planktonic Bacteria Challenged with Disinfectants Commonly Used During Poultry Processing.

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.

Gastrointestinal impactions in backyard poultry.

In contrast to conventional commercial poultry, which are raised primarily in controlled indoor environments, backyard poultry are typically raised in less restricted settings, potentially exposing them to a greater variety of ingestible substances, including multiple types of forage. Consequently, problems such as gastrointestinal impactions caused by ingesta have been noted in backyard poultry. To determine the prevalence of these impactions in backyard poultry, we performed a retrospective database search for autopsy submissions to the California Animal Health and Food Safety laboratory system and found that gastrointestinal impaction was associated with the death of 42 backyard poultry cases (40 chickens, 1 turkey, and 1 goose) from January 2013 to July 2018. In 32 of these 42 (76%) cases, the impaction was caused by fibrous plant material, 7 (17%) by compacted feed, and 3 (7%) by miscellaneous ingesta (tortilla, plastic, and wood shavings). The large proportion of grass impactions indicate that foraging is the predominant source of impaction material in backyard poultry, and that long grasses may be a significant health hazard for poultry. Backyard, pasture-raised, and free-range poultry producers are advised to maintain short pastures, avoid feeds that may expand in the gastrointestinal tract, and provide adequate grit to prevent impactions.

Transcriptome Analysis of Salmonella Heidelberg after Exposure to Cetylpyridinium Chloride, Acidified Calcium Hypochlorite, and Peroxyacetic Acid.

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.

Characterization of an Outbreak of Infectious Coryza (Avibacterium paragallinarum) in Commercial Chickens in Central California.

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.

Caracterización de un brote de coriza infecciosa (Avibacterium paragallinarum) en pollos comerciales en la parte central de California. En el año 2017, la sede en Turlock del Sistema de Laboratorios de Salud Animal y Seguridad Alimentaria de California recibió un aumento significativo en el número de casos de necropsia por coriza infecciosa, con un total de 54 casos, incluyendo casos provenientes de pollos de engorde comerciales (n = 40), gallinas de postura comerciales (n = 11) y aves de traspatio (n = 3). Las parvadas de gallinas de postura positivas para coriza infecciosa se distribuyeron en los condados adyacentes de Merced y Stanislaus, mientras que las parvadas de pollos de engorde se concentraron en el condado de Merced. Las parvadas de traspatio estaban ubicadas en los condados de Alameda y Sacramento. La presentación clínica y patológica fue consistente con coriza infecciosa, aunque también se observaron lesiones septicémicas. Se aisló Avibacterium paragallinarum y se identificó mediante PCR en el tracto respiratorio y también de sitios extrarespiratorios. Las infecciones polimicrobianas relacionadas con otros virus (virus de la bronquitis infecciosa, virus de la enfermedad infecciosa de la bolsa) y bacterias (Mycoplasma spp., Escherichia coli, Ornithobacterium rhinotracheale, Gallibacterium anatis biovar haemolytica) fueron reportadas comúnmente. Trece aislamientos seleccionados de A. paragalinarum se caracterizaron con éxito como serovar C (esquema de Page) y serovar C2 (esquema de Kume). Estos aislamientos Compartieron por PCR un consenso intergénico repetitivo enterobacterial (ERIC) único, que difiere de las cuatro cepas de referencia y mostraron valores constantes de concentración mínima inhibitoria alta para tetraciclina, lo que sugiere un origen común de un solo clon. Con base en estos resultados, siempre se deben implementar y ajustar estándares de bioseguridad altos y la inmunización adecuada de parvadas susceptibles de edades múltiples, según sea necesario. La importancia de las parvadas de traspatio no debe subestimarse debido a su función epidemiológica especial.

Feeding and lighting practices on small-scale extensive pastured poultry commercial farms in the United States.

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.

Drug residues in poultry meat: A literature review of commonly used veterinary antibacterials and anthelmintics used in poultry.

Poultry meat is widely consumed throughout the world and production practices often include the administration of pharmaceutical products. When appropriate, extra-label drug use of medications is necessary, but scientifically derived drug withdrawal intervals must be observed so that poultry meat is not contaminated with drug residues which could pose health risks to consumers. Over the past decade, there has been increased advocacy for judicious use of antimicrobial drugs for treating food animals. Judicious use of medications is commonly referred to as practices that reduce antibiotic resistance, but also includes residue avoidance. In that light, many investigators have performed scientific studies and have published estimated pharmacokinetic parameters for veterinary medications used in commercial avian species. This manuscript is a review of medication classes that have been studied in poultry (mostly chickens) with an emphasis on drug residue depletion in poultry meat.