Assessment of Chicken Carcass Microbiome Responses During Processing in the Presence of Commercial Antimicrobials Using a Next Generation Sequencing Approach

Pectin or chitosan coating fortified with eugenol reduces Campylobacter jejuni on chicken wingettes and modulates expression of critical survival genes

Campylobacter jejuni infection in humans is strongly associated with the consumption of contaminated poultry products. With increasing consumer demand for minimally processed and natural product, there is a need for novel intervention strategies for controlling C. jejuni. Antimicrobial coatings are increasingly being used for preventing food contamination due to their efficacy and continuous protection of product. This study investigated the efficacy of pectin and chitosan coating fortified with eugenol to reduce C. jejuni on chicken wingettes. Pectin, chitosan, and eugenol are generally recognized as safe status compounds derived from berries, crustaceans, and cloves respectively. Each wingette was inoculated with a mixture of 4 wild-type strains of C. jejuni (approximately 10⁷ CFU/sample) and randomly assigned to controls, pectin (3%), chitosan (2%), eugenol (0.5, 1, or 2%), or their combinations. Following 1 min of coating, wingettes were air-dried, vacuum sealed, and sampled on 0, 1, 3, 5, and 7 d of refrigerated storage for C. jejuni and aerobic counts (n = 5 wingettes/treatment/d). In addition, the effect of treatments on wingette color and expression of C. jejuni survival/virulence genes was evaluated. All 3 doses of eugenol or chitosan significantly reduced C. jejuni and aerobic bacteria from 0 d through 7 d. Incorporation of 2% eugenol in chitosan improved coating efficiency and reduced C. jejuni counts by approximately 3 Log CFU/sample at the end of 7 d of storage (P < 0.05). Similarly, the antimicrobial efficacy of pectin was improved by 2% eugenol and the coating reduced C. jejuni by approximately 2 Log CFU/sample at 7 d of storage. Chitosan coating with 2% eugenol also showed greater reductions of total aerobic counts as compared to individual treatments of eugenol and chitosan. No significant difference in the color of chicken wingettes was observed between treatments. Exposure of C. jejuni to eugenol, chitosan, or combination significantly modulated select genes encoding for motility, quorum sensing, and stress response. Results demonstrate the potential of pectin or chitosan coating fortified with eugenol as a postharvest intervention against C. jejuni contamination on poultry products.

Potential for Prebiotics as Feed Additives to Limit Foodborne Campylobacter Establishment in the Poultry Gastrointestinal Tract

Campylobacter as an inhabitant of the poultry gastrointestinal tract has proven to be difficult to reduce with most feed additives. In-feed antibiotics have been taken out of poultry diets due to the negative reactions of consumers along with concerns regarding the generation of antibiotic resistant bacteria. Consequently, interest in alternative feed supplements to antibiotics has grown. One of these alternatives, prebiotics, has been examined as a potential animal and poultry feed additive. Prebiotics are non-digestible ingredients by host enzymes that enhance growth of indigenous gastrointestinal bacteria that elicit metabolic characteristics considered beneficial to the host and depending on the type of metabolite, antagonistic to establishment of pathogens. There are several carbohydrate polymers that qualify as prebiotics and have been fed to poultry. These include mannan-oligosaccharides and fructooligosaccharides as the most common ones marketed commercially that have been used as feed supplements in poultry. More recently, several other non-digestible oligosaccharides have also been identified as possessing prebiotic properties when implemented as feed supplements. While there is evidence that prebiotics may be effective in poultry and limit establishment of foodborne pathogens such as Salmonella in the gastrointestinal tract, less is known about their impact on Campylobacter. This review will focus on the potential of prebiotics to limit establishment of Campylobacter in the poultry gastrointestinal tract and future research directions.

Developments in Rapid Detection Methods for the Detection of Foodborne Campylobacter in the United States

The accurate and rapid detection of Campylobacter spp. is critical for optimal surveillance throughout poultry processing in the United States. The further development of highly specific and sensitive assays to detect Campylobacter in poultry matrices has tremendous utility and potential for aiding the reduction of foodborne illness. The introduction and development of molecular methods such as polymerase chain reaction (PCR) have enhanced the diagnostic capabilities of the food industry to identify the presence of foodborne pathogens throughout poultry production. Further innovations in various methodologies, such as immune-based typing and detection as well as high throughput analyses, will provide important epidemiological data such as the identification of unique or region-specific Campylobacter. Comparable to traditional microbiology and enrichment techniques, molecular techniques/methods have the potential to have improved sensitivity and specificity, as well as speed of data acquisition. This review will focus on the development and application of rapid molecular methods for identifying and quantifying Campylobacter in U.S. poultry and the emergence of novel methods that are faster and more precise than traditional microbiological techniques.

Establishment of a Standardized 16S rDNA Library Preparation to Enable Analysis of Microbiome in Poultry Processing Using Illumina MiSeq Platform

The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety. This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.

Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms

Commercial poultry abattoirs were evaluated to determine the efficacy of the multi-hurdle antimicrobial strategy employed to reduce the microbial load present on incoming broilers from the farm. As next generation sequencing (NGS) has been recently employed to characterize the poultry production system, this study utilized 16S High throughput sequencing (HTS) and quantitative plating data to profile the microbiota of chicken carcasses and determine the efficacy of the multi-hurdle antimicrobial system. Aerobic plate count (APC) and Enterobacteriaceae (EB) microbial counts were quantified from whole bird carcass rinsates (WBCR). The remaining rinsates underwent microbiome analysis using 16S rRNA gene fragments on an Illumina MiSeq and were analyzed by Quantitative Insights into Microbial Ecology (QIIME). The key stages of processing were determined to be at rehang, pre-chill, and post-chill as per the Salmonella Reduction Regulation (75 Fed. Reg. 27288-27294). The APC microbial data from rehang, pre-chill, and post-chill were mean log 4.63 CFU/mL, 3.21 CFU/mL, and 0.89 CFU/mL and EB counts were mean log 2.99 CFU/mL, 1.95 CFU/mL, and 0.35 CFU/mL. NGS of WBCR identified 222 Operational Taxonomic Units' (OTU's) of which only 23 OTU's or 10% of the population was recovered post-chill. Microbiome data suggested a high relative abundance of Pseudomonas at post-chill. Additionally, Pseudomonas, Enterobacteriaceae, and Weeksellaceae Chryseobacterium have been identified as potential indicator organisms having been isolated from all processing abattoirs and sampling locations. This study provides insight into the microbiota of commercial broilers during poultry processing.

The nasal microbiota in health and disease: variation within and between subjects

Chronic rhinosinusitis (CRS) affects approximately 5% of the adult population in Western societies and severely reduces the patient's quality of life. The role of bacteria in the pathogenesis of this condition has not yet been established with certainty. However, recent reports of bacterial and fungal biofilms in CRS highlight a potential role for these microorganisms. In this study, 16S rRNA gene-targeted amplicon pyrosequencing and qPCR were used to determine the composition and abundance, respectively, of the sinus microbiota within 9 patients with CRS and 6 healthy individuals. Within-patient variability was also investigated by sampling from anterior nares, inferior turbinate, and middle meatus on each side of the sinuses. Our results indicate that more of the variation in bacterial composition can be explained by inter-personal differences, rather than sampling location or even disease status. In addition, bacterial community diversity was significantly lower in CRS samples compared to those from healthy subjects, whereas bacterial load was not associated with disease status. Although members of the genera Corynebacterium and Staphylococcus were prevalent in the majority of samples (including healthy subjects), the large amount of variation observed between individuals, particularly within the CRS cohort, suggests that an imbalance or dysbiosis in community structure could be the driving force behind the disease. Ultimately, understanding the causes of variation within the sinus microbiota may lead to more personalized treatment options for CRS.

The nasal microbiota in health and disease: variation within and between subjects

Chronic rhinosinusitis (CRS) affects approximately 5% of the adult population in Western societies and severely reduces the patient's quality of life. The role of bacteria in the pathogenesis of this condition has not yet been established with certainty. However, recent reports of bacterial and fungal biofilms in CRS highlight a potential role for these microorganisms. In this study, 16S rRNA gene-targeted amplicon pyrosequencing and qPCR were used to determine the composition and abundance, respectively, of the sinus microbiota within 9 patients with CRS and 6 healthy individuals. Within-patient variability was also investigated by sampling from anterior nares, inferior turbinate, and middle meatus on each side of the sinuses. Our results indicate that more of the variation in bacterial composition can be explained by inter-personal differences, rather than sampling location or even disease status. In addition, bacterial community diversity was significantly lower in CRS samples compared to those from healthy subjects, whereas bacterial load was not associated with disease status. Although members of the genera Corynebacterium and Staphylococcus were prevalent in the majority of samples (including healthy subjects), the large amount of variation observed between individuals, particularly within the CRS cohort, suggests that an imbalance or dysbiosis in community structure could be the driving force behind the disease. Ultimately, understanding the causes of variation within the sinus microbiota may lead to more personalized treatment options for CRS.