A Novel Slope-Matrix-Graph Algorithm to Analyze Compositional Microbiome Data.

Networks are widely used to represent relationships between objects, including microorganisms within ecosystems, based on high-throughput sequencing data. However, challenges arise with appropriate statistical algorithms, handling of rare taxa, excess zeros in compositional data, and interpretation. This work introduces a novel Slope-Matrix-Graph (SMG) algorithm to identify microbiome correlations primarily based on slope-based distance calculations.

Digital PCR assay for the specific detection and estimation of contamination levels in poultry rinse.

Strains of are a frequent cause of foodborne illness and are known to contaminate poultry products. Most testing methods can qualitatively detect and cannot quantify or estimate the load in samples. Therefore, the aim of this study was to standardize and validate a partitioned-based digital PCR (dPCR) assay for the detection and estimation of contamination levels in poultry rinses.

Evaluating the effects of virulence genotype, swarming motility, and multi-locus sequence types of Escherichia coli on layer chicken embryos.

Aims: To determine the effects of swarming motility (SM) and multi-locus sequence types (MLST) on the main effect of virulence genotype of Escherichia coli through an embryos lethality assay between the 12th and 18th days of incubation.

Methods And Results: We collected 58 E. coli isolates from asymptomatic commercial hens (n = 42) and lesions of colibacillosis cases (n = 16), then classified their virulence genotype as avirulent, moderately virulent, virulent-healthy, and virulent-colibacillosis categories by the presence of five virulence-associated genes (iroN, ompT, hlyF, iutA, and iss).

Detection and Distribution of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in Campylobacter jejuni Isolates from Chicken Livers.

Campylobacter jejuni is the leading foodborne bacterial pathogen that causes human gastroenteritis worldwide linked to the consumption of undercooked broiler livers. Application of bacteriophages during poultry production has been used as an alternative approach to reduce contamination of poultry meat by Campylobacter. To make this approach effective, understanding the presence of the bacteriophage sequences in the CRISPR spacers in C.

A Survey of the Levels of Selected Metals in U.S. Meat, Poultry, and Siluriformes Fish Samples Taken at Slaughter and Retail, 2017-2022.

The U.S. Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS) conducts surveillance of metallic elements in U.

Synergistic Effects of Essential Oils and Organic Acids against Contamination in Poultry Feed.

Organic acids and essential oils are commonly used in the poultry industry as antimicrobials and for their beneficial effects on gut health, growth performance, and meat quality. A common postharvest storage fungal colonist, , contaminates corn, the primary component of poultry feed, with the highly detrimental mycotoxin, aflatoxin. Aflatoxin adversely affects poultry feed intake, feed conversion efficiency, weight gain, egg production, fertility, hatchability, and poultry meat yield.

Exudate From Retail Chicken Liver Packaging Allows for Survival of Naturally Occurring Campylobacter, Coliforms, and Aerobic Microorganisms Under Drying Conditions.

Campylobacter spp. are a leading cause of human foodborne illness associated with chicken meat products in the United States. Chicken livers, including exudate from packaging, commonly carry Campylobacter and could be a source of illness if mishandled.

Use of automated capillary immunoassays for quantification of antibodies in chicken sera against recombinant Salmonella enterica serotype Heidelberg proteins.

The classic immunoblot technique is an important tool for identification and characterization of target proteins. However, a standard protocol for this classic immunoblot assay involves many steps that may cause experimental variations in each step and make quantification of antibodies in sera difficult. A capillary electrophoresis-based immunoblot system was developed to reduce potential problems in variations during the experimental process, enable protein identification in an automatic manner and quantitate various isotypes of antibodies in sera.

Classification between live and dead foodborne bacteria with hyperspectral microscope imagery and machine learning.

Identifying live foodborne bacteria is essential for ensuring food safety and preventing foodborne illnesses. This study investigated the use of hyperspectral microscope imaging and deep learning methods to accurately distinguish between live and dead foodborne bacteria based on their spectral and morphological features. Three deep learning models, Fusion-Net I, II, and III, were developed and evaluated for their ability to classify live and dead bacterial cells of six pathogenic strains, including Escherichia coli (EC), Listeria innocua (LI), Staphylococcus aureus (SA), Salmonella Enteritidis (SE), Salmonella Heidelberg (SH), and Salmonella Typhimurium (ST).

Buffered Peptone Water Formulation Does Not Influence Growth of pESI-positive Salmonella enterica Serovar Infantis.

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.

Serotype Screening of Subspecies I by Intergenic Sequence Ribotyping (ISR): Critical Updates.

(1) Background: Foodborne illness from subspecies I is most associated with approximately 32 out of 1600 serotypes. While whole genome sequencing and other nucleic acid-based methods are preferred for serotyping, they require expertise in bioinformatics and often submission to an external agency. Intergenic Sequence Ribotyping (ISR) assigns serotype to in coordination with information freely available at the National Center for Biotechnology Information.

Resilience of Chemistry: An Introduction to the Agricultural and Food Chemistry Technical Program at the 262nd American Chemical Society National Hybrid Meeting & Exposition, Both Online and in Atlanta, Georgia.

This is the third special issue of the () based on the Agricultural and Food Chemistry Division (AGFD) technical program, at the 262nd American Chemical Society National Meeting. This was the first national meeting held in a hybrid format, both virtually and in-person in Atlanta, Georgia, U.S.

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.

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.

Through the Looking Glass: Genome, Phenome, and Interactome of .

This review revisits previous concepts on biological phenomenon contributing to the success of the subspecies I as a pathogen and expands upon them to include progress in epidemiology based on whole genome sequencing (WGS). Discussion goes beyond epidemiological uses of WGS to consider how phenotype, which is the biological character of an organism, can be correlated with its genotype to develop a knowledge of the interactome. Deciphering genome interactions with proteins, the impact of metabolic flux, epigenetic modifications, and other complex biochemical processes will lead to new therapeutics, control measures, environmental remediations, and improved design of vaccines.

Water properties and marinade uptake in broiler pectoralis major with the woody breast condition.

To provide insight into the mechanisms by which the woody breast (WB) condition reduces marinade uptake, water properties of normal (NOR) and WB meat were investigated using TD-NMR. Broiler Pectoralis major was marinated with either water, 0.625% sodium tripolyphosphate, 5% NaCl, or 5% NaCl + 0.

Characterisation of Flavour Attributes in Egg White Protein Using HS-GC-IMS Combined with E-Nose and E-Tongue: Effect of High-Voltage Cold Plasma Treatment Time.

Egg white protein (EWP) is susceptible to denaturation and coagulation when exposed to high temperatures, adversely affecting its flavour, thereby influencing consumers' decisions. Here, we employ high-voltage cold plasma (HVCP) as a novel nonthermal technique to investigate its influence on the EWP's flavour attributes using E-nose, E-tongue, and headspace gas-chromatography-ion-mobilisation spectrometry (HS-GC-IMS) due to their rapidness and high sensitivity in identifying flavour fingerprints in foods. The EWP was investigated at 0, 60, 120, 180, 240, and 300 s of HVCP treatment time.

Survey of Meat Collected from Commercial Broiler Processing Plants Suggests Low Levels of Semicarbazide Can Be Created during Immersion Chilling.

Abstract: Semicarbazide (SEM) is routinely employed as an indicator for the use of nitrofurazone, a banned antimicrobial. The validity of SEM as a nitrofurazone marker has been scrutinized because of other possible sources of the compound. Nonetheless, a U.

Effect of Plasma-Activated Solution Treatment on Cell Biology of and Quality of Fresh Lettuces.

This study aimed to investigate effects of plasma-activated solution (PAS) on the cell biology of and qualities of fresh lettuce leaves. PAS was prepared by dielectric barrier discharge plasma and incubated with for 10-30 min or with lettuces for 10 min. Effects on cell biology were evaluated with microscopic images, cell integrity, and chemical modification of cellular components.

Plasma-activated water: A novel frozen meat thawing media for reducing microbial contamination on chicken and improving the characteristics of protein.

To solve the problems of microbial contamination and protein loss caused by the conventional thawing method, plasma-activated water (PAW) and ultrasound were applied. Changes in microorganisms, protein loss, oxidation, degradation, digestion, and lipid oxidation were measured to evaluate the practicability of novel thawing treatments. Compared with the conventional thawing treatment, PAW thawing and ultrasound in combination with PAW thawing resulted in the reduction of the bacterium for 0.

Prevalence and Characterization of Quinolone Resistance in Campylobacter spp. Isolates in Chicken Livers from Retail Stores in Georgia, USA.

Abstract: Campylobacter is a bacterial pathogen that causes human foodborne illnesses worldwide, and outbreaks have been associated with consumption of undercooked chicken livers. The objectives of this study were to compare two PCR assays of 250 Campylobacter isolates for identification to species, to assess antibiotic resistance of the isolates, and to analyze genetic diversity of the quinolone resistance determining regions (QRDRs) of the isolates. A double-blind design was used to identify the species of Campylobacter; 181 (72%) of the isolates were identified as Campylobacter jejuni, and 69 (28%) isolates were identified as Campylobacter coli by both PCR assays.

Inactivation kinetics and cell envelope damages of foodborne pathogens Listeria monocytogenes and Salmonella Enteritidis treated with cold plasma.

In recent years, more attention has been paid to the application of cold plasma (CP) in eliminating foodborne pathogenic bacteria. This work investigated CP effects on inactivation kinetics and cell envelopes of Listeria monocytogenes (L. monocytogenes) and Salmonella Enteritidis (S.

Prevalence of Listeria Species and Listeria monocytogenes on Raw Produce Arriving at Frozen Food Manufacturing Facilities.

Abstract: The ubiquity of Listeria monocytogenes in the environment affects the food industry and presents concerns for frozen food facilities. This study determined the prevalence and numbers of Listeria species and L. monocytogenes on raw produce arriving at frozen food facilities.

Evaluation of multi blade shear (MBS) for determining texture of raw and cooked broiler breast fillets with the woody breast myopathy.

The objective of this study was to evaluate a novel multi-blade Shear (MBS) method for measuring texture properties of both raw and cooked broiler fillets (pectoralis major) with the woody breast (WB) myopathy. A total of 180 broiler breast fillets (60 normal [NOR], 60 moderate WB [MOD], and 60 severe WB [SEV]) in two meat states (fresh never-frozen, n = 144; frozen/thawed, n = 36) were chosen based on their WB scores. In each trial, half of the fillets were used for measuring raw meat texture and the other half for cooked meat texture measurement.