2014 Naive Broiler CAFO Study for Agricultural Antibiotic Resistance in Mississippi State, Mississippi Conventional commercial broiler production involves the rearing of more than 20,000 broilers in a single confined space, atop bedding material such as pine shavings or rice hulls, for approximately 6.5 weeks. This environment is known for harboring pathogens and antibiotic resistant bacteria, but studies have focused on previously established houses. A concerted effort by the broiler industry has involved the scaling back of antibiotic use on-farm, but this has only been a recent occurrence. In the current study, a set of three naïve houses were followed from inception through 11 broiler flocks and monitored for ambient climatic conditions, bacterial pathogens, and antibiotic resistance. Within the first 3 weeks of the first flock cycle, 100% of litter samples were positive for Salmonella and Listeria while Campylobacter was culture negative. In all likelihood, given that pre flock bedding and soil levels were negative for pathogens and 4-5 orders of magnitude lower for other indicators, chicks most likely provided the colonizing bacteria. The influence of intra-house location was minor with only watering lines and side walls influencing some pathogen and indicator levels. Most bacterial groups experienced the typical cyclical pattern of litter contamination seen in other studies. This study represents a first of its kind view into the time required for bacterial pathogens and antibiotic resistance to colonize and establish in naïve broiler houses.

The agricultural baseline database provides longrun, 10-year projections from USDA's annual long-term projections report. The database covers projections for major field crops (corn, sorghum, barley, oats, wheat, rice, soybeans, and upland cotton), and livestock (beef, pork, poultry and eggs, and dairy).

This repository contains all data and code required to reproduce the growth curve-fitting analysis from the manuscript: McMillan, E. A., Berrang, M. E., Read, Q. D., Rasamsetti, S., Richards, A. K., Shariat, N. W., & Frye, J. G. (2022). Buffered peptone water formulation does not influence growth of pESI-positive Salmonella enterica serovar Infantis. Journal of Food Protection, 100033. https://doi.org/10.1016/j.jfp.2022.100033 Manuscript abstract Salmonella enterica is a major cause of human foodborne illness and is often attributed to poultry food sources. S. enterica serovar Infantis, specifically those carrying the pESI plasmid, has become a frequently isolated serotype from poultry meat samples at processing and has caused numerous recent human infections. In 2016, the USDA Food Safety and Inspection Service changed the official sampling method for raw poultry products from BPW to using neutralizing BPW (nBPW) as the rinsing agent in order to prevent residual antimicrobial effects from acidifying and oxidizing processing aids. This change was contemporaneous to the emergence of pESI-positive ser. Infantis as a prevalent serovar in poultry, prompting some to question if nBPW could be selecting for this prevalent serovar. We performed two experiments: a comparison of ser. Infantis growth in BPW versus nBPW, and a simulation of regulatory sampling methods. We found that when inoculated into both broths, ser. Infantis initially grows slightly slower in nBPW than in BPW but little difference was seen in abundance after six hours of growth. Additionally, use of nBPW to simulate poultry rinse sample and overnight cold shipping to a regulatory lab did not affect survival or subsequent growth of ser. Infantis in BPW. We concluded that the change in USDA-FSIS methodology to include nBPW in sampling procedures has likely not affected the emergence of S. ser. Infantis as a prevalent serovar in chicken and turkey meat product samples. Contents All necessary data are in a single comma-separated file, Sal_Infantis_growth_curve_data_EAM.csv. All R code is in a single RMarkdown document, salmonella_growth_curve_fitting.Rmd. The RMarkdown contains code to read and process the data, produce exploratory plots, fit the model, do all hoc calculations with the posterior output, and produce figures and tables from the manuscript. Salmonella Infantis growth data: This is a comma-separated file containing data needed to reproduce the growth curve fitting analysis. Columns are: Strain: numerical ID of strain (see Table 1 in manuscript) Colony_Forming_Units_per_mL_(A, B, C): columns 2-4 are three replicate measurements of colony forming units per mL taken from the same sample at the same time. Media: whether nBPW or BPW was used in the growth medium Time_hours: time in hours ranging from 0-6. RMarkdown document with all analysis code: This RMarkdown document contains code to read and process the data, produce exploratory plots, fit the model, do all hoc calculations with the posterior output, and produce figures and tables from the manuscript. Software versions This was run on Windows 10, R version 4.1.2. Models were fit using CmdStan version 2.28.2, with brms version 2.17.0, cmdstanr version 0.4.0, emmeans version 1.7.3, and tidybayes version 3.0.2. Program information National Program: Food Safety (108) Project Plan Number: 6040-32000-085-000-D

This is USDA-ARS data from the publication, "Characterization of particle size distributions and water-soluble ions in particulate matter measured at a broiler farm." This study was conducted in June of 2018. Data included here are from several measurements: Gas-phase ammonia measurements measured by an electrochemical sensor (Cairpol) in part-per-billion (ppb) with 1 minute time interval. Particle number concentration inside and outside the house measured by two optical particle counters (MetOne) in number per cubic centimeter (mg/cc) with 20 second interval. Particles were measured from 0.5-10 micrometers in 8 size bins. Particle number concentration measured by a scanning mobility particle sizer (TSI) and given as the differential number per size bin over 80 bins from 10-500 nanometers with a 5 minute time interval. Water-soluble ions in particulate matter measured by an ambient ion monitor (URG) measured in microgram per cubic meter with a 1 hour time interval. Resources in this dataset: Resource Title: Ammonia Sensor Measurements File Name: SensorNH3.txt Resource Title: Optical Particle Counter 1 File Name: OpticalParticleCounter1.txt Resource Title: Optical Particle Counter 2 File Name: OpticalParticleCounter2.txt Resource Title: Scanning Mobility Particle Sizer Data (Matrix) File Name: SMPS Data.txt Resource Title: Scanning Mobility Particle Sizer Axes File Name: SMPS Axes.txt Resource Title: AIM Particulate Chemical Composition File Name: AIM Composition.txt

Data are the individual group values for oral and cloacal virus shedding and antibody titers for reach treatment group from: Mo et al., The pathogenicity and transmission of live bird market H2N2 avian influenza viruses in chickens, Pekin ducks, and guinea fowl. Vet Mic 260:109180, 2021. https://doi.org/10.1016/j.vetmic.2021.109180 Methods: Six H2N2 low pathogenic avian influenza viruses from US LBMs were selected based on recency and to represent the different genotypes present in the live birds markets during the time period (i.e., the presence or absence of a NA stalk deletion): A/duck/PA/14-030488-5/2014 (Dk/PA/14), A/chicken/NY/16-032621-2/2016 (Ck/NY/16), A/chicken/CT/17-008911-4/2017 (Ck/CT/17), A/chicken/NY/18-002471-4/2018 (CK/NY/02471/18), A/chicken/NY/18-042097-3/2018 (Ck/NY/042097/18) and A/chicken/NY/19-012787-1/2019 (Ck/NY/19). Isolates were evaluated in White Leghorn chickens (Gallus gallus), guinea fowl (Numida meleagris) and Pekin ducks (Anas platyrhynchos). Chickens and guinea fowl were challenged at 4 weeks of age and Pekin ducks were challenged at 2 weeks of age with 6log10 of virus by the intra-choanal route. “Contact” birds, which were hatch-mates of the inoculated birds, were co-housed with the inoculated birds 24hrs post inoculation to evaluate transmission. Viral loads in OP and CL swabs collected at 2, 4, 7, 10, and 14 days post inoculation were determined by quantitative real-time reverse-transcriptase polymerase chain reaction (qRT-PCR). RNA was extracted from swabs using the MagMAX96 Viral RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA) and the KingFisher Flex Magnetic Particle Processing System (Thermo Fisher Scientific), with an additional wash step to remove inhibitors (Das et al., 2009). The qRT‐PCR for AIV detection was conducted based on the standard USDA M gene AIV qRT‐PCR procedure (Spackman et al., 2002) using an Applied Biosystems® 7500 Fast Real‐Time PCR system (Thermo Fisher Scientific). Cycle threshold (Ct) values were determined by the 7500 Fast Software v2.3. For relative quantification, Ct values were converted to titer equivalents based on the standard curve method (Larionov et al., 2005). Values were established from ten-fold dilutions of the same titrated stock of the virus used to challenge the birds. The limit of detection was determined to be 0.8Log10 per reaction. Serological testing for antibodies to the virus utilized the hemagglutination inhibition (HI) assays using homologous antigens were performed to quantify antibody responses with serum collected from chickens, guinea fowl and Pekin ducks at 14 dpi based on the standard protocol (OIE, 2019). HI titers were reported as reciprocal log2 titers, and titers greater than 3 log2 (1:8) were considered positive.

Annual Progress Reports on Salmonella and Campylobacter Testing of Selected Raw Meat and Poultry Products

Pulse-field gel electrophoresis (PFGE) Campylobacter reports for FSIS Raw Products from fiscal year (FY) 2016 to FY2019. See FSIS website for additional information.

This quarterly report summarizes chemical residue results for the United States National Residue Program for meat, poultry, and egg products. The results in this report cover the domestic (scheduled and inspector-generated) and import sampling programs. Data is updated quarterly. See the FSIS website for additional information.

These data provide additional demographic information about FSIS regulated establishments. Additional demographic data are also available in the FSIS Meat, Poultry, and Egg Inspection Directory (MPI). The Meat, Poultry and Egg Product Inspection Directory is a listing of establishments that produce meat, poultry, and/or egg products regulated by USDA's Food Safety and Inspection Service (FSIS).

FSIS’ FoodKeeper application educates users about food and beverages storage to help them maximize the freshness and quality of these items. By helping users understand food storage, the application empowers consumers to choose storage methods that extend the shelf life of their items. By doing so users will be able to keep items fresh longer than if they were not stored properly.

Import refusals for products regulated by FSIS. Current files are updated monthly; archive files are updated quarterly. See the FSIS website for additional information.

Import volume for products re-inspected by FSIS at the port of entry. Both current and archive files are posted quarterly. See the FSIS website for additional information.

The Meat, Poultry and Egg Product Inspection Directory is a listing of establishments that produce meat, poultry, and/or egg products regulated by USDA's Food Safety and Inspection Service (FSIS) pursuant to the Federal Meat Inspection Act, the Poultry Products Inspection Act, and the Egg Products Inspection Act. The directory is updated weekly, and the current edition replaces all previous editions.

Salmonella verification testing for individual establishments and the aggregated data for Young Chicken and Turkey Carcasses, Raw Chicken Parts, and NRTE Comminuted Poultry establishments. Data is updated on the 20th of every month, or the following business day if the 20th falls on a weekend or holiday. See the FSIS website for additional information.

Establishment specific sampling results for FSIS Ready-to-Eat (RTE) sampling projects. Current data is updated quarterly; archive data is updated annually. See the FSIS website for additional information.

Establishment specific sampling results for FSIS’ routine risk-based Listeria monocytogenes (RLm) sampling projects. Current data is updated quarterly; archive data is updated annually. See the FSIS website for additional information.

Pulse-field gel electrophoresis (PFGE) Salmonella reports for FSIS Raw Products from fiscal year (FY) 2016 to FY2019. See FSIS website for additional information.

Percent positive and serotype quarterly sampling information for Salmonella and Campylobacter in FSIS Raw Products. Reports are updated quarterly. See FSIS website for additional information.

FSIS calculates prevalence, volume weighted percent positive, or percent positive calculations for microbial pathogens in FSIS regulated products that are currently sampled through existing sampling projects. FSIS intends to provide new calculations each quarter using the prior 12 months of sampling data. See the FSIS website for additional information.

This datasets summarizes and lists all the recalls of meat and poultry products produced by FSIS federally inspected establishments for the calendar year. Recalls are characterized by date, recall class, product, reason and pounds recalled. More detailed information can be found in each recall announcement posted on the FSIS website.

Nutrient recycling is fundamental to sustainable agricultural systems, but few mechanisms exist to ensure that surplus manure nutrients from animal feeding operations are transported for use on nutrient-deficient croplands. As a result, manure nutrients concentrate in locations where they can threaten environmental health and devalue manure as a fertilizer resource. This data set is from a study advances the concept of the “manureshed” – the lands surrounding animal feeding operations onto which manure nutrients can be redistributed to meet environmental, production, and economic goals. Manuresheds can be managed at multiple scales, for example, on farms with both animals and crops, among animal farms and crop farms within a county, or even among animal farms and crop farms in distant counties. With a focus on redistribution among counties, we classified the 3109 counties of the contiguous United States by their capacity to either supply manure phosphorus (P) and nitrogen (N) from confined livestock production (“sources”) or to assimilate and remove excess P and N via crops (“sinks”) [see data for N tonnes, P tonnes, N kg/ha, P kg/ha]. Manure nutrient source counties were identified in 40 of the 48 states, with a substantial concentration in the southern US. Source counties for manure P greatly outnumbered source counties for manure N (390 vs. 100), and 99 of the 100 manure N source counties were also source counties for manure P. Conversely, sink counties for manure N outnumbered sink counties for manure P (2766 vs. 2317). We used the P balances of the source and sink counties to delineate four manuresheds dominated by various combinations of confined hog, poultry, dairy, and beef industries [see data for Manuresheds (tonnes)]. The four manuresheds differed in the transport distances needed to assimilate excess manure P from their respective source areas (from 147 ± 51 km for a beef dominated manureshed to 368 ± 140 km for a poultry dominated manureshed), highlighting the need for systems-level strategies to promote manure nutrient recycling that operate across local, county, regional, and national scales.

The National Animal Health Monitoring System (NAHMS) Program Unit conducts national studies on the health, management, and productivity of United States domestic livestock and poultry populations.

Note: Updates to this data product are discontinued. This data set provides farmgate and wholesale prices for select organic and conventional fruits and vegetables, wholesale prices for organic and conventional poultry (broilers) and eggs, as well as f.o.b. and spot prices for organic grain and feedstuffs. Prices are based on those reported by USDA Agricultural Marketing Service Market News, Organic Food Business News, and USDA National Agricultural Statistics Service.

Quick Stats is the National Agricultural Statistics Service's (NASS) online, self-service tool to access complete results from the 1997, 2002, 2007, and 2012 Censuses of Agriculture as well as the best source of NASS survey published estimates. The census collects data on all commodities produced on U.S. farms and ranches, as well as detailed information on expenses, income, and operator characteristics. The surveys that NASS conducts collect information on virtually every facet of U.S. agricultural production.

Quick Stats API is the programmatic interface to the National Agricultural Statistics Service's (NASS) online database containing results from the 1997, 2002, 2007, and 2012 Censuses of Agriculture as well as the best source of NASS survey published estimates. The census collects data on all commodities produced on U.S. farms and ranches, as well as detailed information on expenses, income, and operator characteristics. The surveys that NASS conducts collect information on virtually every facet of U.S. agricultural production.

Establishment specific sampling results for FSIS' Ready-to-Eat Intensified Verification Testing. Current data is updated quarterly; archive data is updated annually. See the FSIS website for additional information.

Recent USDA/ARS patented technologies on animal production and protection that are available for licensing are described, including summary, contact, benefits, and applications. Updated June 2018.

Recent USDA/ARS patented technologies on food processing and products that are available for licensing are described, including summary, contact, benefits, and applications. Updated June 2018.