Results of the 2016 Indianapolis Biodiversity Survey, Marion County, Indiana

Surprising biodiversity can be found in cities, but urban habitats are understudied. We report on a bioblitz conducted primarily within a 24-hr period on September 16 and 17, 2016 in Indianapolis, Indiana, USA. The event focused on stretches of three waterways and their associated riparian habitat: Fall Creek (20.6 ha; 51 acres), Pleasant Run (23.5 ha; 58 acres), and Pogue’s Run (27.1 ha; 67 acres). Over 75 scientists, naturalists, students, and citizen volunteers comprised 14 different taxonomic teams. Five hundred ninety taxa were documented despite the rainy conditions. A brief summary of the methods and findings are presented here. Detailed maps of survey locations and inventory results are available on the Indiana Academy of Science website (https://www.indianaacademyofscience.org/)

Deep Sensitivity Analysis for Objective-Oriented Combinatorial Optimization

Pathogen control is a critical aspect of modern poultry farming, providing important benefits for both public health and productivity. Effective poultry management measures to reduce pathogen levels in poultry flocks promote food safety by lowering risks of food-borne illnesses. They also support animal health and welfare by preventing infectious diseases that can rapidly spread and impact flock growth, egg production, and overall health. This study frames the search for optimal management practices that minimize the presence of multiple pathogens as a combinatorial optimization problem. Specifically, we model the various possible combinations of management settings as a solution space that can be efficiently explored to identify configurations that optimally reduce pathogen levels. This design incorporates a neural network feedback-based method that combines feature explanations with global sensitivity analysis to ensure combinatorial optimization in multiobjective settings. Our preliminary experiments have promising results when applied to two real-world agricultural datasets. While further validation is still needed, these early experimental findings demonstrate the potential of the model to derive targeted feature interactions that adaptively optimize pathogen control under varying real-world constraints.Comment: The 2023 International Conference on Computational Science & Computational Intelligence (CSCI'23

Towards Interpreting Multi-Objective Feature Associations

Understanding how multiple features are associated and contribute to a specific objective is as important as understanding how each feature contributes to a particular outcome. Interpretability of a single feature in a prediction may be handled in multiple ways; however, in a multi-objective prediction, it is difficult to obtain interpretability of a combination of feature values. To address this issue, we propose an objective specific feature interaction design using multi-labels to find the optimal combination of features in agricultural settings. One of the novel aspects of this design is the identification of a method that integrates feature explanations with global sensitivity analysis in order to ensure combinatorial optimization in multi-objective settings. We have demonstrated in our preliminary experiments that an approximate combination of feature values can be found to achieve the desired outcome using two agricultural datasets: one with pre-harvest poultry farm practices for multi-drug resistance presence, and one with post-harvest poultry farm practices for food-borne pathogens. In our combinatorial optimization approach, all three pathogens are taken into consideration simultaneously to account for the interaction between conditions that favor different types of pathogen growth. These results indicate that explanation-based approaches are capable of identifying combinations of features that reduce pathogen presence in fewer iterations than a baseline.Comment: The 18th Annual IEEE International Systems Conference 2024 (IEEE SYSCON 2024

Using Farm Practice Variables as Predictors of Listeria spp. Prevalence in Pastured Poultry Farms

Predictive models offer food scientists, farmers, and processors tools to help identify variables that lead to an increase in the food safety risk of a product. Foodborne pathogens, such as Listeria spp., pose a major problem for the pastured poultry industry. Currently, there is a lack of understanding of what farm practices lead to higher prevalence of Listeria spp. This study constructed random forest (RF) models to predict the prevalence of Listeria spp. in pastured poultry farming environments and the final broiler product based on major farm practices and variables. Feces, soil, and whole carcass rinse samples were collected from 11 farms in the southeastern United States and evaluated for Listeria spp. presence. The preharvest sample RF model identified the time of year and age of the broiler flock at time of sampling as factors of increased probability of Listeria spp. presence in feces and soil samples. The final product RF model identified brood feed and the presence of chlorine in processing rinse water as the two most important variables associated with an increased likelihood of Listeria spp. presence. Both the preharvest RF model and final sample RF model performed well on a held-out test set, with area under the receiver operating characteristic curve values of 0.876 and 0.887, respectively. The presented models showed the usefulness of RF models in a food safety context. Both RF models will help pastured poultry farmers and processors guide control strategies to manage Listeria contamination in pastured poultry farms and products

Applications of Microbiome Analyses in Alternative Poultry Broiler Production Systems

While most of the focus on poultry microbiome research has been directed toward conventional poultry production, there is increasing interest in characterizing microbial populations originating from alternative or non-conventional poultry production. This is in part due to the growing general popularity in locally produced foods and more specifically the attractiveness of free-range or pasture raised poultry. Most of the focus of microbiome characterization in pasture flock birds has been on live bird production, primarily on the gastrointestinal tract. Interest in environmental impacts on production responses and management strategies have been key factors for comparative microbiome studies. This has important ramifications since these birds are not only raised under different conditions, but the grower cycle can be longer and in some cases slower growing breeds used. The impact of different feed additives is also of interest with some microbiome-based studies having examined the effect of feeding these additives to birds grown under pasture flock conditions. In the future, microbiome research approaches offer unique opportunities to develop better live bird management strategies and design optimal feed additive approaches for pasture flock poultry production systems

Essential Oils as an Intervention Strategy to Reduce Campylobacter in Poultry Production: A Review

Campylobacter is a major foodborne pathogen and can be acquired through consumption of poultry products. With 1.3 million United States cases a year, the high prevalence of Campylobacter within the poultry gastrointestinal tract is a public health concern and thus a target for the development of intervention strategies. Increasing demand for antibiotic-free products has led to the promotion of various alternative pathogen control measures both at the farm and processing level. One such measure includes utilizing essential oils in both pre- and post-harvest settings. Essential oils are derived from plant-based extracts, and there are currently over 300 commercially available compounds. They have been proposed to control Campylobacter in the gastrointestinal tract of broilers. When used in concentrations low enough to not influence sensory characteristics, essential oils have also been proposed to decrease bacterial contamination of the poultry product during processing. This review explores the use of essential oils, particularly thymol, carvacrol, and cinnamaldehyde, and their role in reducing Campylobacter concentrations both pre- and post-harvest. This review also details the suggested mechanisms of action of essential oils on Campylobacter

Listeria Occurrence and Potential Control Strategies in Alternative and Conventional Poultry Processing and Retail

Listeria monocytogenes is a psychrotrophic Gram positive organism that is considered one of the more critical foodborne pathogens of public health concern. To prevent illness the USDA and FDA enforce a zero-tolerance policy for Listeria on ready-to-eat foods such as delicatessen meats and poultry. Regardless, L. monocytogenes can still be isolated from food production facilities and retail products, indicating that current sanitation methods are not always sufficient. Both conventional and alternative poultry production and processing systems have also been identified as potential sources of Listeria spp. Concerns associated with alternative poultry production and processing can be further exacerbated by limitations on sanitation and available antimicrobials for usage in organic and natural poultry products. Furthermore, mobile poultry processing units often process organic and small-scale poultry farms that are not able to be processed by conventional standing facilities. These alternative production facilities and their products are often exempt from federal inspection, due to processing a relatively low number of carcasses. Due to these exemptions, it is unknown if sufficient sanitation is applied in these alternative processing facilities to prevent L. monocytogenes contamination. Organic processing restrictions may also impact which sanitizers and antimicrobials can be utilized. This review describes variations between conventional and mobile poultry processing units in conjunction with how L. monocytogenes may persist in the processing environment and on retail products. This review will also examine alternative antimicrobials proven to be effective against Listeria spp. and potentially be acceptable for use in alternative poultry production systems

A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples

The efficacy of DNA extraction protocols can be highly dependent upon both the type of sample being investigated and the types of downstream analyses performed. Considering that the use of new bacterial community analysis techniques (e.g., microbiomics, metagenomics) is becoming more prevalent in the agricultural and environmental sciences and many environmental samples within these disciplines can be physiochemically and microbiologically unique (e.g., fecal and litter/bedding samples from the poultry production spectrum), appropriate and effective DNA extraction methods need to be carefully chosen. Therefore, a novel semi-automated hybrid DNA extraction method was developed specifically for use with environmental poultry production samples. This method is a combination of the two major types of DNA extraction: mechanical and enzymatic. A two-step intense mechanical homogenization step (using bead-beating specifically formulated for environmental samples) was added to the beginning of the “gold standard” enzymatic DNA extraction method for fecal samples to enhance the removal of bacteria and DNA from the sample matrix and improve the recovery of Gram-positive bacterial community members. Once the enzymatic extraction portion of the hybrid method was initiated, the remaining purification process was automated using a robotic workstation to increase sample throughput and decrease sample processing error. In comparison to the strict mechanical and enzymatic DNA extraction methods, this novel hybrid method provided the best overall combined performance when considering quantitative (using 16S rRNA qPCR) and qualitative (using microbiomics) estimates of the total bacterial communities when processing poultry feces and litter samples.Keywords: Environmental, DNA extraction, Feces, qPCR, Litter, Microbiomics, Molecular biology, Semi-automated, PoultryKeywords: Environmental, DNA extraction, Feces, qPCR, Litter, Microbiomics, Molecular biology, Semi-automated, Poultr

The characterization of Salmonella enterica serotypes isolated from the scalder tank water of a commercial poultry processing plant: Recovery of a multidrug-resistant Heidelberg strain

The recent multistate outbreak of a multidrug-resistant (MDR) Salmonella Heidelberg strain from commercial poultry production highlights the need to better understand the reservoirs of these zoonotic pathogens within the commercial poultry production and processing environment. As part of a larger study looking at temporal changes in microbial communities within the major water tanks within a commercial processing facility, this paper identifies and characterizes Salmonella enterica isolated from the water in a final scalder tank at 3 times during a typical processing day: prior to the birds entering the tank (start), halfway through the processing day (mid), and after the final birds were scalded (end). Over 3 consecutive processing days, no Salmonella were recovered from start-of-day water samples, while a total of 56 Salmonella isolates were recovered from the mid-day and end-of-day scalder water samples. Traditional and newer PCR-based serotyping methods eventually identified these isolates as either group C3 S. Kentucky (n = 45) and group B S. Heidelberg (n = 11). While none of the S. Kentucky isolates possessed any resistances to the antimicrobials tested, all S. Heidelberg isolates were found to be multidrug resistant to 5 specific antimicrobials representing 3 antimicrobial classes. Due to the potential public health impact of S. Heidelberg and the recent nationwide poultry-associated outbreak of multidrug-resistant S. Heidelberg, future studies should focus on understanding the transmission and environmental growth dynamics of this serotype within the commercial poultry processing plant environment.Keywords: S. Heidelberg, Scalder water, Multidrug resistanc