Monitoring Behaviors of Broiler Chickens at Different Ages with Deep Learning.

Animal behavior monitoring allows the gathering of animal health information and living habits and is an important technical means in precision animal farming. To quickly and accurately identify the behavior of broilers at different days, we adopted different deep learning behavior recognition models. Firstly, the top-view images of broilers at 2, 9, 16 and 23 days were obtained.

An ensemble learning approach to identify pastured poultry farm practice variables and soil constituents that promote prevalence.

Animal sourced foods including contaminated poultry meat and eggs contribute to human non-typhoidal salmonellosis, a foodborne zoonosis. Prevalence of in pastured poultry production systems can lead to contamination of the final product. Identification of farm practices that affect prevalence is critical for implementing control measures to ensure the safety of these products.

Detection and Genome Sequence Analysis of Avian Metapneumovirus Subtype A Viruses Circulating in Commercial Chicken Flocks in Mexico.

Avian metapneumoviruses (aMPV subtypes A-D) are respiratory and reproductive pathogens of poultry. Since aMPV-A was initially reported in Mexico in 2014, there have been no additional reports of its detection in the country. Using nontargeted next-generation sequencing (NGS) of FTA card-spotted respiratory samples from commercial chickens in Mexico, seven full genome sequences of aMPV-A (lengths of 13,288-13,381 nucleotides) were de novo assembled.

Comparison between LASSO and RT methods for prediction of generic E. coli concentration in pastured poultry farms.

Though most strains of E. coli are non-pathogenic components of the intestinal microbiome, certain pathogenic E. coli strains are the cause of diseases and outbreaks.

Complete genome sequences of two clinical isolates from Egypt carrying on IncP and IncX4 plasmids.

Colistin is a last-resort antibiotic used in the treatment of multidrug resistant Gram-negative bacteria. However, the activity and efficacy of colistin has been compromised by the worldwide spread of the mobile colistin resistance genes ( to ). In this study, two clinical strains, named CAI51, and CAI73, harbored , showed multidrug-resistant phenotypes (with colistin MIC = 4 μg/ml), and belonged to phylogroup D: multilocus sequence type 1011 (ST1011) and phylogroup A: ST744, respectively.

Preharvest Environmental and Management Drivers of Multidrug Resistance in Major Bacterial Zoonotic Pathogens in Pastured Poultry Flocks.

Due to nutritional benefits and perceived humane ways of treating the animals, the demand for antibiotic-free pastured poultry chicken has continued to be steadily rise. Despite the non-usage of antibiotics in pastured poultry broiler production, antibiotic resistance (AR) is reported in zoonotic poultry pathogens. However, factors that drive multidrug resistance (MDR) in pastured poultry are not well understood.

Research Note: Internal organ colonization by Salmonella Enteritidis in experimentally infected layer pullets reared at different stocking densities in indoor cage-free housing.

Contamination of eggs by Salmonella has often been identified as a source of food-borne human illness. S. Enteritidis is deposited inside developing eggs when invasive infections of laying hens reach the reproductive organs.

4-Oxo-2-nonenal (4-ONE)-Induced Degradation of Bovine Skeletal Muscle Proteins.

Lipids are an important component of meat, as they provide desirable sensory characteristics and nutritional benefits. However, lipids are susceptible to degradation through oxidation and produce toxic oxidative byproducts. 4-Oxo-2-nonenal (4-ONE) is an oxidative byproduct that is highly reactive and cytotoxic.

Using E. coli population to predict foodborne pathogens in pastured poultry farms.

Escherichia coli shows the potential of indicating foodborne pathogens. The purpose of this study is to investigate the association between E. coli and foodborne pathogens such as Campylobacter, Salmonella, and Listeria in pastured poultry farms, as well as in related processing facilities.

Reducing zoonotic avian influenza transmission at household poultry slaughter using a behaviour change tool for limited literacy audiences.

Human infections in Egypt with highly pathogenic avian influenza (HPAI) likely due to airborne transmission of HPAI virus (HPAIV) during home slaughter of poultry predominately affect women and children, who are the primary caregivers of household poultry. This study developed a safe contained poultry slaughter procedure to reduce airborne HPAIV and zoonotic infections and simultaneously created an educational outreach tool for teaching the modified procedure. The tool designed for limited literacy audiences used two illustrated posters and handouts for teaching the safe contained poultry slaughter procedure.

Subclinical Doses of Combined Fumonisins and Deoxynivalenol Predispose Inoculated Broilers to Necrotic Enteritis.

Fumonisins (FB) and deoxynivalenol (DON) are mycotoxins which may predispose broiler chickens to necrotic enteritis (NE). The objective of this study was to identify the effects of subclinical doses of combined FB and DON on NE. A total of 480 day-old male broiler chicks were divided into four treatment groups; 1) control group (basal diet + ); 2) necrotic enteritis group (basal diet + ); 3) FB + DON group (basal diet + 3 mg/kg FB + 4 mg/kg DON + ); and 4) FB + DON + NE group (basal diet + 3 mg/kg FB + 4 mg/kg DON + ).

Genome Sequence Variations of Infectious Bronchitis Virus Serotypes From Commercial Chickens in Mexico.

New variants of infectious bronchitis viruses (IBVs; ) continuously emerge despite routine vaccinations. Here, we report genome sequence variations of IBVs identified by random non-targeted next generation sequencing (NGS) of vaccine and field samples collected on FTA cards from commercial flocks in Mexico in 2019-2021. Paired-ended sequencing libraries prepared from rRNA-depleted RNAs were sequenced using Illumina MiSeq.

Evaluation of mechanical cervical dislocation, captive bolt, carbon dioxide, and electrical methods for individual on-farm euthanasia of broiler breeders.

Efficacious euthanasia by applying manual cervical dislocation can be difficult on large and mature poultry. The challenge with using manual cervical dislocation is that the strength required to hold heavy poultry and swiftly apply cervical dislocation can be physically impossible for most people. Therefore, alternative methods of euthanasia are needed for mature and large poultry.

Increased Prevalence of Infantis Isolated from Raw Chicken and Turkey Products in the United States Is Due to a Single Clonal Lineage Carrying the pESI Plasmid.

Infantis has recently become one of the most common serotypes of Salmonella isolated in the U.S. from raw meat samples collected in processing facilities and in retail stores.

CAMPYAIR, a New Selective, Differential Medium for spp. Isolation without the Need for Microaerobic Atmosphere.

spp. are considered the most frequent bacterial cause of acute gastroenteritis worldwide. Although the diarrhea produced by these bacteria is self-limiting, the pathogen has been associated with severe long-term sequelae following acute signs and symptoms of the illness.

Non-point source fecal contamination from aging wastewater infrastructure is a primary driver of antibiotic resistance in surface waters.

Antibiotic resistance is a global threat to human health. Many surface water resources are environmental hotspots of antibiotic resistant gene (ARG) transfer, with agricultural runoff and human waste highlighted as common sources of ARGs to aquatic systems. Here we quantified fecal marker genes and ARGs in 992 stream water samples collected seasonally during a 5-year period from 115 sites across the Upper Oconee watershed (Georgia, USA), an area characterized by gradients of agricultural and urban development.

Detection of Aflatoxin B in Single Peanut Kernels by Combining Hyperspectral and Microscopic Imaging Technologies.

To study the dynamic changes of nutrient consumption and aflatoxin B (AFB) accumulation in peanut kernels with fungal colonization, macro hyperspectral imaging technology combined with microscopic imaging was investigated. First, regression models to predict AFB contents from hyperspectral data ranging from 1000 to 2500 nm were developed and the results were compared before and after data normalization with Box-Cox transformation. The results indicated that the second-order derivative with a support vector regression (SVR) model using competitive adaptive reweighted sampling (CARS) achieved the best performance, with R = 0.

Non-target RNA depletion strategy to improve sensitivity of next-generation sequencing for the detection of RNA viruses in poultry.

PCR-based assays have become the benchmark for detecting pathogens of poultry and other livestock; however, these techniques are limited in their ability to detect multiple infecting agents, provide limited genetic information on the pathogen, and, for RNA viruses, must be reviewed frequently to assure high sensitivity and specificity. In contrast, untargeted, high-throughput sequencing can rapidly detect all infecting agents in a sample while providing genomic sequence information to allow more in-depth characterization of viruses. Although next-generation sequencing (NGS) offers many advantages, one of its primary limitations is low sensitivity to pathogens given the abundance of host and other non-target sequences in sequencing libraries.

Breast Meat Fatty Acid Profiling and Proteomic Analysis of Beijing-You Chicken During the Laying Period.

The disparity in fatty acids (FA) composition exhibits a significant impact on meat quality, however, the molecular regulatory mechanisms underlying this trait in chicken are far from clear. In this study, a total of 45 female Beijing-You chicken (BYC) hens, fed on the same diet, were collected at the slaughter age of 150, 300, or 450 days (D150, D300, and D450) from sexual maturation stage to culling stage (15 birds per age). Gas chromatography-mass spectrometry (GC-MS) and tandem mass tag labeling technology based on liquid chromatography mass spectrometry (TMT-LC-MS/MS) analysis strategies were applied to profile FA compositions and to compare differential expressed proteins (DEPs) between these different slaughter ages, respectively.

Near-Complete Genome Sequence of an Avian Orthoavulavirus Type 13 Strain Isolated in South Korea in 2020.

We report the near-complete genome sequence of an avian orthoavulavirus 13 (AOAV-13) strain isolated from a wild goose fecal sample collected in South Korea in early 2020. The AOAV-13 sequence had a unique 3' trailer region, including an 84-nucleotide (nt) deletion and a 24-nt insertion, compared to the most closely related Chinese genome sequence from 2015.

Distribution and Transfer of Plasmid Replicon Families among Multidrug-Resistant and from Poultry.

The presence and transfer of plasmids from commensal bacteria to more pathogenic bacteria may contribute to the dissemination of antimicrobial resistance. However, the prevalence of plasmids from commensal bacteria, such as the enterococci, in food animals remains largely unknown. In this study, the diversity and prevalence of plasmid families from multidrug-resistant (MDR; resistance to three or more antimicrobials) enterococci from poultry carcasses were determined.

Resistance Genes, Plasmids, Multilocus Sequence Typing (MLST), and Phenotypic Resistance of Non-Typhoidal (NTS) Isolated from Slaughtered Chickens in Burkina Faso.

The emergence of antimicrobial-resistant bacteria in developing countries increases risks to the health of both such countries' residents and the global community due to international travel. It is consequently necessary to investigate antimicrobial-resistant pathogens in countries such as Burkina Faso, where surveillance data are not available. To study the epidemiology of antibiotic resistance in , 102 strains isolated from slaughtered chickens were subjected to whole-genome sequencing (WGS) to obtain information on antimicrobial resistance (AMR) genes and other genetic factors.

Enrichment and Direct Plating for Detection of Campylobacter in Chicken Liver Rinse and Exudate.

Abstract: Foodborne campylobacteriosis has been traced to undercooked chicken liver dishes; thus, it is important to use the best available culture methods when testing for the presence of Campylobacter. We compared two Campylobacter enrichment broths-Bolton formulation and Neogen formulation-in combination with three selective plating media-Campy-Cefex, Campy-Line and RF Campylobacter agars-for detection of Campylobacter from fresh retail chicken livers. In each of three experiments, nine replicate tubs of chicken livers were sampled by drawing exudate and a pooled rinse of five whole liver lobes.

Transcriptomic Responses of to Lactam and Lactone Xenobiotics.

The important cereal crops of maize, rye, and wheat constitutively produce precursors to 2-benzoxazolinone, a phytochemical having antifungal effects towards many species. However, can tolerate 2-benzoxazolinone by converting it into non-toxic metabolites through the synergism of two previously identified gene clusters, and . Inspired by the induction of these two clusters upon exposure to 2-benzoxazolinone, RNA sequencing experiments were carried out by challenging individually with 2-benzoxazolinone and three related chemical compounds, 2-oxindole, 2-coumaranone, and chlorzoxazone.

Microfluidic Sampling and Biosensing Systems for Foodborne and .

Developments of portable biosensors for field-deployable detections have been increasingly important to control foodborne pathogens in regulatory environment and in early stage of outbreaks. Conventional cultivation and gene amplification methods require sophisticated instruments and highly skilled professionals; while portable biosensing devices provide more freedom for rapid detections not only in research laboratories but also in the field; however, their sensitivity and specificity are limited. Microfluidic methods have the advantage of miniaturizing instrumental size while integrating multiple functions and high-throughput capability into one streamlined system at low cost.