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

Microbial dynamics of South Korean beef and surroundings along the supply chain based on high-throughput sequencing

Microbiological safety and quality of beef is crucial as beef can serve as a reservoir for a variety of bacteria, including spoilage-related and foodborne pathogens. Controlling microbial contamination is a critical aspect of food quality and safety, but it is difficult to prevent as there are several potential sources of contamination from production to distribution. In this study, the microbiological ecology of cattle/beef and associated environmental samples (n = 69) were trace-investigated to reveal microbiome shifts in cattle/beef and possible cross-contaminants throughout the entire supply chain using 16S rRNA gene sequencing. Pseudomonas, Psychrobacter, and Acinetobacter, known as spoilage bacteria, opportunistic pathogens, or antibiotic-resistant bacteria, were the main microorganisms present in cattle/beef, and Staphylococcus became abundant in the final products. The dominance of Acinetobacter and Pseudomonas was noticeable in the slaughtered carcasses and slaughterhouse environment, indicating that the slaughterhouse is a critical site where hygienic practices are required to prevent further contamination. Taxonomic similarities between cattle/beef and several environmental samples, as well as diversity analysis, presented a high potential for microbial transmission. Source tracking identified environmental samples that primarily contributed to the microbiota of cattle/beef. Farm floor (48%), workers' gloves (73%), and carcass splitters (20%) in the slaughterhouse were found to be major sources influencing the microbiome of cattle/beef at the farm, slaughterhouse, and processing plant, respectively. These findings demonstrated the dynamics of bacterial communities in cattle/beef according to stage and detected potential contamination sources, which may aid in a better understanding and control of microbial transmission in beef production.

Microbial contamination pathways in a poultry abattoir provided clues on the distribution and persistence of Arcobacter spp

The consumption of contaminated poultry meat is a significant threat for public health, as it implicates in foodborne pathogen infections, such as those caused by Arcobacter. The mitigation of clinical cases requires the understanding of contamination pathways in each food process and the characterization of resident microbiota in the productive environments, so that targeted sanitizing procedures can be effectively implemented. Nowadays these investigations can benefit from the complementary and thoughtful use of culture- and omics-based analyses, although their application in situ is still limited. Therefore, the 16S-rRNA gene-based sequencing of total DNA and the targeted isolation of Arcobacter spp. through enrichment were performed to reconstruct the environmental contamination pathways within a poultry abattoir, as well as the dynamics and distribution of this emerging pathogen. To that scope, broiler's neck skin and caeca have been sampled during processing, while environmental swabs were collected from surfaces after cleaning and sanitizing. Metataxonomic survey highlighted a negligible impact of fecal contamination and a major role of broiler's skin in determining the composition of the resident abattoir microbiota. The introduction of Arcobacter spp. in the environment was mainly conveyed by this source rather than the intestinal content. Arcobacter butzleri represented one of the most abundant species and was extensively detected in the abattoir by both metataxonomic and enrichment methods, showing higher prevalence than other more thermophilic Campylobacterota. In particular, Arcobacter spp. was recovered viable in the plucking sector with high frequency, despite the adequacy of the sanitizing procedure.IMPORTANCEOur findings have emphasized the persistence of Arcobacter spp. in a modern poultry abattoir and its establishment as part of the resident microbiota in specific environmental niches. Although the responses provided here are not conclusive for the identification of the primary source of contamination, this biogeographic assessment underscores the importance of monitoring Arcobacter spp. from the early stages of the production chain with the integrative support of metataxonomic analysis. Through such combined detection approaches, the presence of this pathogen could be soon regarded as hallmark indicator of food safety and quality in poultry slaughtering.

Interventions to reduce Salmonella and Campylobacter during chilling and post-chilling stages of poultry processing: a systematic review and meta-analysis

Salmonella and Campylobacter are common bacterial hazards causing foodborne illnesses worldwide. A large proportion of Salmonella and Campylobacter illnesses are attributed to contaminated poultry products that are mishandled or under cooked. Processing interventions such as chilling and post-chill dip are critical to reducing microbial contamination of poultry. A comprehensive search of the literature published between 2000 and 2021 was conducted in the databases Web of Science, Academic Search Complete, and Academic OneFile. Studies were included if they were in English and investigated the effects of interventions against Salmonella and/or Campylobacter on whole carcasses and/or parts during the chilling or post-chill stages of poultry processing. Random-effects meta-analyses were performed using the "meta" package in the R programming language. Subgroup analyses were assessed according to outcome measure reported, microorganism tested, processing stage assessed, and chemical treatment used. The results included 41 eligible studies. Eighteen studies reported results of 28 separate interventions against Salmonella and 31 reported results of 50 separate interventions against Campylobacter. No significant difference (P> 0.05) was observed when comparing the combined mean difference of all interventions targeting Salmonella to the combined mean difference of all interventions targeting Campylobacter or when comparing chilling times within each pathogen subgroup. For analyses examining antimicrobial additives, peroxyacetic acid (PAA) had the largest reduction against Salmonella population regardless of chilling time (P< 0.05). PAA also had the largest reduction against Campylobacter population and prevalence during primary chilling (P< 0.01). Air chilling showed a lower reduction for Campylobacter than any immersion chilling intervention (P< 0.05). Chilling time and antimicrobial used during poultry processing had varying effects depending on the pathogen and outcome measure investigated (concentration or prevalence). High heterogeneity and low sample numbers in most analyses suggest that more high-quality research that is well-designed and has transparent reporting of methodology and results is needed to corroborate the results.

Exploiting the microbiota of organic and inorganic acid-treated raw poultry products to improve shelf-life

Introduction

Targeted amplicon sequencing of the 16S rRNA delineates the complex microbial interactions that occur during food spoilage, providing a tool to intensively screen microbiota response to antimicrobial processing aids and interventions. The current research determines the microbiota and spoilage indicator (total aerobes and lactic acid bacteria; LAB) response to inorganic and organic antimicrobial intervention use on the shelf-life of fresh, never-frozen, skin-on, bone-in chicken wings.

Methods

Wings (n=200) were sourced from local processor and either not treated (NT) or treated with 15-s dips of tap water (TW), organic (peracetic acid; PAA), inorganic acids (sodium bisulfate; SBS), and their combination (SBS + PAA). Wings were stored (4°C) and rinsed in neutralizing Buffered Peptone Water (BPW) for 1 min on d 0, 7, 14, and 21 post-treatment. Spoilage indicators, aerobic mesophiles and LAB, were quantified from rinsates. Genomic DNA of d 14 and 21 rinsates were extracted, and V4 of 16S rRNA gene was sequenced. Sequences were analyzed using QIIME2.2019.7. APC and LAB counts were reported as Log10 CFU/g of chicken and analyzed in R Studio as a General Linear Model using ANOVA. Pairwise differences were determined using Tukey's HSD (P£0.05).

Results

Spoilage was indicated for all products by day 21 according to APC counts (>7 Log10 CFU/g); however, wings treated with SBS and SBS + PAA demonstrated a 7-day extended shelf-life compared to those treated with NT, TW, or PAA. The interaction of treatment and time impacted the microbial diversity and composition (p < 0.05), with those treated with SBS having a lower richness and evenness compared to those treated with the controls (NT and TW; p < 0.05, Q < 0.05). On d 14, those treated with SBS and SBS + PAA had lower relative abundance of typical spoilage population while having a greater relative abundance of Bacillus spp. (~70 and 50% of population; ANCOM p < 0.05). By d 21, the Bacillus spp. populations decreased below 10% of the population among those treated with SBS and SBS + PAA.

Discussion

Therefore, there are differential effects on the microbial community depending on the chemical intervention used with organic and inorganic acids, impacting the microbial ecology differently.

Bacterial profile of pork from production to retail based on high-throughput sequencing

Pork is a common vehicle for foodborne pathogens, including Salmonella spp. and Yersinia enterocolitica. Cross-contamination can occur at any stage of the pork production chain, from farm to market. In the present study, high-throughput sequencing was used to characterize bacterial profiles and track their changes along the whole supply chain. Tracked meat samples (pig on the farm, carcass in the slaughterhouse, unprocessed carcass and processed meat in the processing plant, and fresh pork at the local retail stores) and their associated environmental samples (e.g., water, floor, feed, feces, and workers' gloves) were collected from sequential stages (n = 96) and subjected to 16S rRNA metataxonomic analyses. At the farm, a total of 652 genera and 146 exclusive genera were identified in animal and environmental samples (pig, drain, floor, fan, and feces). Based on beta diversity analysis, it was demonstrated that the microbial composition of animal samples collected at the same processing step is similar to that of environmental samples (e.g., drain, fan, feces, feed, floor, gloves, knives, tables, and water). All animal and environmental samples from the slaughterhouse were dominated by Acinetobacter (55.37 %). At the processing plant, belly meat and neck meat samples were dominated by Psychrobacter (55.49 %). At the retail level, key bacterial players, which are potential problematic bacteria and important members with a high relative abundance in the samples, included Acinetobacter (8.13 %), Pseudomonas (6.27 %), and Staphylococcus (2.13 %). In addition, the number of confirmed genera varied by more than twice that identified in the processing plant. Source tracking was performed to identify bacterial contamination routes in pork processing. Animal samples, including the processing plant's carcass, the pig from the farm, and the unwashed carcass from the slaughterhouse (77.45 %), along with the processing plant's gloves (5.71 %), were the primary bacterial sources in the final product. The present study provides in-depth knowledge about the bacterial players and contamination points within the pork production chain. Effective control measures are needed to control pathogens and major pollutants at each stage of pork production to improve food safety.

Adaptation of a Commercial Qualitative BAX® Real-Time PCR Assay to Quantify Campylobacter spp. in Whole Bird Carcass Rinses

Poultry is the primary reservoir of Campylobacter, a leading cause of gastroenteritis in the United States. Currently, the selective plating methodology using selective agars, Campy Cefex and Modified Charcoal Cefoperazone Deoxycholate agar, is preferentially used for the quantification of Campylobacter spp. among poultry products. Due to the specific nature of Campylobacter, this methodology is not sensitive, which can lead to skewed detection and quantification results. Therefore, Campylobacter detection and quantification methods are urgently needed. The objective was to develop a shortened enrichment-based quantification method for Campylobacter (CampyQuant™) in post-chill poultry rinsates using the BAX® System Real-Time PCR assay for Campylobacter. The specificity and sensitivity for the detection of C. jejuni, C. coli, and C. lari in pure culture were determined. The BAX® System Real-Time PCR assay consistently detected and identified each species 100% of the time with an enumeration range of 4.00 to 9.00 Log10 CFU/mL. Enrichment time parameters for low-level concentrations (0.00, 1.00, and 2.00 Log10 CFU/mL) of Campylobacter using the BAX® System Real-Time PCR assay were elucidated. It was determined that an enrichment time of 20 h was needed to detect at least 1.00 Log10 CFU/mL of Campylobacter spp. Using the BAX® System Real-Time PCR assay for Campylobacter. As a result, time of detection, detection limits, and enrichment parameters were used to develop the CampyQuant™ linear standard curve using the detected samples from the BAX® System Real-Time PCR assay to quantify the levels in post-chill poultry rinsates. A linear fit equation was generated for each Campylobacter species using the cycle threshold from the BAX® System Real-Time PCR assay to estimate a pre-enrichment of 1.00 to 4.00 Log10 CFU/mL of rinsates detected. The statistical analyses of each equation yielded an R2 of 0.93, 0.76, and 0.94 with a Log10 RMSE of 0.64, 1.09, and 0.81 from C. jejuni, C. coli, and C. lari, respectively. The study suggests that the BAX® System Real-Time PCR assay for Campylobacter is a more rapid, accurate, and efficient alternative method for Campylobacter enumeration.

Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessment

Despite the continuous progress in food science and technology, the global burden of foodborne illnesses remains substantial, with pathogens in food causing millions of infections each year. Traditional microbiological culture methods are inadequate in detecting the full spectrum of these microorganisms, highlighting the need for more comprehensive detection strategies. This review paper aims to elucidate the relationship between foodborne pathogen colonization and the composition of the poultry microbiome, and how this knowledge can be used for improved food safety. Our review highlights that the relationship between pathogen colonization varies across different sections of the poultry microbiome. Further, our review suggests that the microbiome profile of poultry litter, farm soil, and farm dust may serve as potential indicators of the farm environment's food safety issues. We also agree that the microbiome of processed chicken samples may reveal potential pathogen contamination and food quality issues. In addition, utilizing predictive modeling techniques on the collected microbiome data, we suggest establishing correlations between particular taxonomic groups and the colonization of pathogens, thus providing insights into food safety, and offering a comprehensive overview of the microbial community. In conclusion, this review underscores the potential of microbiome analysis as a powerful tool in food safety, pathogen detection, and risk assessment.

Peracetic acid application as an antimicrobial and its residual (HEDP): a holistic approach on the technological characteristics of chicken meat

The most significant occurrence of food-borne diseases is due to Campylobacter and Salmonella contamination from chicken meat, and for this reason, strict regulations about strategies to improve the control of food pathogens are imposed by food safety authorities. Despite the efforts of poultry industry since the beginning of risk analysis and critical control point to reduce the burden of food-borne illness, technological barriers along the way are increasingly necessary to ensure safe food. The aim of this review was to carry out a scientific approach to the influence of peracetic acid (PAA) as an antimicrobial and its toxicological safety, in particular the stabilizer used in the formulation of PAA, 1-hydroxyethylidene 1,1-diphosphonic acid (HEDP), suggesting the possibility of researching the residual HEDP in meat, which would allow the approval of the PAA by the health authorities of several countries that still restrict it. This review also aims to ascertain the effectiveness of PAA, in different cuts and carcasses, by different application methods, comparing the effectiveness of this antimicrobial with other antimicrobials, and its exclusive or combined use, for the decontamination of poultry carcasses and raw parts. The literature results support the popularity of PAA as an effective intervention against pathogenic bacteria during poultry processing.

Evidence of host specificity in Lactobacillus johnsonii genomes and its influence on probiotic potential in poultry

To date, the selection of candidate strains for probiotic development in production animals has been largely based upon screens for desired phenotypic traits. However, increasing evidence indicates that the use of host-specific strains may be important, because coevolution with the animal host better prepares a bacterial strain to colonize and succeed in its respective host animal species. This concept was applied to Lactobacillus johnsonii in commercial poultry production because of its previous correlation with enhanced bird performance. Using 204 naturally isolated chicken- and turkey-source L. johnsonii, we demonstrate that there is a strong phylogenetic signal for coevolution with the animal host. These isolates differ phenotypically, even within host source, and these differences can be correlated with certain L. johnsonii phylogenetic clades. In commercial turkey poults, turkey-specific strains with strong in vitro phenotypes performed better early in life than strains lacking those phenotypes. A follow-up performance trial in broiler chickens demonstrated that chicken-specific strains result in better overall bird performance than nonchicken-specific strains. Collectively, this work provides evidence for the impact of host adaptation on a probiotic strain's potential. Furthermore, this top-down approach is useful for screening larger numbers of isolates for probiotic candidates.

Filter sterilized carcass rinsate for recovery of Salmonella species with various concentrations of cetylpyridinium chloride

Controlling Salmonella in poultry processing continues to be important to processors and consumers. Cetylpyridinium chloride (CPC) has proven to be effective in vitro in controlling Salmonella. This study evaluated the recovery of Salmonella after overnight storage in 4°C filter-sterilized carcass rinsate containing CPC from 0.44 to 909 ppm (μg/mL). Ten Salmonella serotypes (18 strains), of which 6 serotypes are commonly isolated from poultry products, were grown in Bacto-Tryptic Soy Broth overnight at 37°C. Serial dilutions of a CPC/propylene glycol solution were prepared in 24-well tissue culture plates containing filter-sterilized carcass rinsate. Approximately 107 cfu/mL of each Salmonella serotype was added to the appropriate wells. Inoculated plates were stored overnight at 4°C. After storage, triplicate plates of brilliant green agar with sulfapyridine (BGS) were surface inoculated with 10 μL of the contents for each well, streaked for isolation, and incubated at 37°C for 24 h. Three replications were conducted. The presence of typical colonies on BGS plates was recorded as growth and verified through biochemical and serological testing. Of the serotypes chosen, Salmonella Kentucky, Dublin, and Enteritidis were the least resistant to CPC with a median minimum inhibitory concentration (MIC) of 14.22 μg/mL (range from 3.55 to 56.88 μg/mL); S. Typhimurium demonstrated a median MIC of 114.00 μg/mL (range from 28.44 to 114.00 μg/mL). Residual CPC potentially remaining attached to a carcass or in the weep after processing could potentially alter which Salmonella serotype is recovered from a carcass rinse due to different growth patterns during regulatory testing, with a potential for more virulent strains not to be recovered.

Microbial trace investigation throughout the entire chicken supply chain based on metagenomic high-throughput sequencing

As poultry possesses a high risk of contamination by various pathogens and has repeatedly been linked to foodborne outbreaks, ensuring microbiological safety throughout the chicken production chain is essential. In this study, bacterial communities in chickens and associated environments (n = 72), including feces, floors, gloves, and worktables, were trace investigated from the broiler farm, slaughterhouse, meat processing plant, and the market by amplicon sequencing of the V4 region of the 16S rRNA. The bacterial composition in live chickens along the production chain significantly changed across the stages, with distinct microbiota noted at each step. Pseudomonas, Shewanella, Acinetobacter, and Psychrobacter were dominant in the final products. Staphylococcus was abundant in live birds originally (36.83 %) but dramatically decreased after slaughter (3.07 %, 0.06 %, and 0.42 % in slaughtered, processed, and market carcasses, respectively), which may be attributed to defeathering. The proportion of Enterobacteriaceae, Acinetobacter, and Pseudomonas increased from 0.95 %, 0.03 %, and 0.04 % before slaughter to 13.57 %, 34.19 %, and 21.90 %, respectively, after slaughter, highlighting the importance of hygiene management in the succeeding steps. Diversity analysis revealed the possibility of bacterial transmission between samples from the processing plant and the market. Source tracking was performed to identify microbial contamination routes in the chicken microbiome; the major bacterial sources in the final products were the samples from the processing plant (such as processed carcasses, gloves, and worktables), accounting for 93.53 % of the total microbial sources. These results suggest that in-depth knowledge of microbial transmission between chickens and their surroundings can facilitate a precise understanding of microbiological concerns across the poultry production system and help establish safety management measures for the poultry industry.

The Microbial Genetic Diversity and Succession Associated with Processing Waters at Different Broiler Processing Stages in an Abattoir in Australia

The high organic content of abattoir-associated process water provides an alternative for low-cost and non-invasive sample collection. This study investigated the association of microbial diversity from an abattoir processing environment with that of chicken meat. Water samples from scalders, defeathering, evisceration, carcass-washer, chillers, and post-chill carcass rinsate were collected from a large-scale abattoir in Australia. DNA was extracted using the Wizard^® Genomic DNA Purification Kit, and the 16S rRNA v3-v4 gene region was sequenced using Illumina MiSeq. The results revealed that the Firmicutes decreased from scalding to evisceration (72.55%) and increased with chilling (23.47%), with the Proteobacteria and Bacteroidota changing inversely. A diverse bacterial community with 24 phyla and 392 genera was recovered from the post-chill chicken, with Anoxybacillus (71.84%), Megamonas (4.18%), Gallibacterium (2.14%), Unclassified Lachnospiraceae (1.87%), and Lactobacillus (1.80%) being the abundant genera. The alpha diversity increased from scalding to chilling, while the beta diversity revealed a significant separation of clusters at different processing points (p = 0.01). The alpha- and beta-diversity revealed significant contamination during the defeathering, with a redistribution of the bacteria during the chilling. This study concluded that the genetic diversity during the defeathering is strongly associated with the extent of the post-chill contamination, and may be used to indicate the microbial quality of the chicken meat.

Microbial investigation of aquacultured olive flounder (Paralichthys olivaceus) from farm to table based on high-throughput sequencing

The microbial ecologies of fish, such as the olive flounder (Paralichthys olivaceus), one of the most widely consumed fish in East Asia, remain to be elucidated. The microbiome of olive flounder and related environmental samples (i.e., feed, water, workers' aprons and gloves) were collected from six different sources (i.e., a fish farm, a transporting truck, a Wando market and restaurant, and a Seoul market and restaurant). These samples (n = 102) were investigated at various farm-to-distribution stages based on their 16S rRNA sequences. The microbial communities of fish from the farms and trucks were dominated by Photobacterium (>86 %) and showed distinct differences from fish from the Wando and Seoul markets and restaurants. There was also a significant difference in fish microbiomes according to geographical location. The relative abundances of Shewanella, Acinetobacter, Enterobacteriaceae, and Pseudomonas increased as the distribution and consumption stages of the supply chain advanced. The percentages of Shewanella (24.74 %), Acinetobacter (18.32 %), and Enterobacteriaceae (11.24 %) in Wando, and Pseudomonas (42.98 %) in Seoul markets and restaurants implied the importance of sanitation control in these areas. Alpha and beta diversity results corresponded to taxonomic analyses and showed the division of two groups (i.e., fish from the production and transporting stage (farm and truck fish) and fish from the distribution and consumption stages (market and restaurant fish)). The present study provides an in-depth understanding of olive flounder and its environmental microbiomes and suggests control measures to improve food safety.

Quality and Processability of Modern Poultry Meat

The poultry meat industry has gone through many changes. It moved from growing dual-purpose birds (meat and egg production) taking ~110 days to reach 1.2 kg 100 years ago, to developing specialized meat breeds that grow to 2.5 kg within ~40 days. It also moved from selling ~80% whole birds to mostly selling cut up and further processed products in the Western world. This necessitated building large, centralized processing plants, capable of processing 15,000 birds per hr on a single line (60 years ago only 2500), that require higher bird uniformity (size, color, texture). Furthermore, consumer demand for convenient products resulted in introducing many cut-up fresh poultry (some companies have 500 SKU) and further processed products (chicken nuggets did not exist 50 years ago). Those developments were possible due to advancements in genetics, nutrition, medicine, and engineering at the farm and processing plant levels. Challenges keep on coming and today a rise in myopathies (e.g., so called woody breast, white striping, spaghetti meat), requires solutions from breeders, farmers, and processing plants, as more automation also requires more uniformity. This review focuses on the changes and challenges to the processing industry segment required to keep supplying high quality poultry to the individual consumer.

Consequences of Implementing Neutralizing Buffered Peptone Water in Commercial Poultry Processing on the Microbiota of Whole Bird Carcass Rinses and the Subsequent Microbiological Analyses

In 2016, the United States Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS) established guidelines which modified the Buffered Peptone Water (BPW) rinsate material to include additional compounds that would better neutralize residual processing aids and allow for better recovery of sublethal injured Salmonella spp. cells. While the added compounds improved the recovery of Salmonella spp., specific data to understand how the new rinse agent, neutralizing Buffered Peptone Water (nBPW), impacts the recovery of other microorganisms such as Campylobacter spp. and indicator microorganisms are lacking. Therefore, this study evaluated the impact of rinse solutions (BPW or nBPW) used in Whole Bird Carcass rinsate (WBCR) collections on the subsequent microbiome and downstream culturing methodologies. Carcasses exiting a finishing chiller were rinsed in 400 ml of BPW or nBPW. Resulting rinsates were analyzed for Enterobacteriaceae (EB), Salmonella, and Campylobacter spp. prevalence and total aerobic bacteria (APC) and EB load. The 16S rDNA of the rinsates and the matrices collected from applied microbiological analyses were sequenced on an Illumina MiSeq^®. Log₁₀-transformed counts were analyzed in JMP 15 using ANOVA with means separated using Tukey’s HSD, and prevalence data were analyzed using Pearson’s χ² (P ≤ 0.05). Diversity and microbiota compositions (ANCOM) were analyzed in QIIME 2.2019.7 (P ≤ 0.05; Q ≤ 0.05). There was an effect of rinsate type on the APC load and Campylobacter spp. prevalence (P < 0.05), but not the quantity or prevalence of EB or Salmonella spp. prevalence. There were differences between the microbial diversity of the two rinsate types and downstream analyses (P < 0.05). Additionally, several taxa, including Streptococcus, Lactobacillus, Aeromonas, Acinetobacter, Clostridium, Enterococcaceae, Burkholderiaceae, and Staphylococcaceae, were differentially abundant in paired populations. Therefore, the rinse buffer used in a WBCR collection causes proportional shifts in the microbiota, which can lead to differences in results obtained from cultured microbial populations.

Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies

Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, and bioinformatics-in addition to the traditional considerations when conducting an animal science study-makes microbiome studies sometimes intimidating due to the intersection of different fields. The objective of this review is to serve as a jumping-off point for those animal scientists less familiar with 16S rRNA gene sequencing and analyses and to bring up common issues and concerns that arise when planning an animal microbiome study from design through analysis. This review includes an overview of 16S rRNA gene sequencing, its advantages, and its limitations; experimental design considerations such as study design, sample size, sample pooling, and sample locations; wet lab considerations such as field handing, microbial cell lysis, low biomass samples, library preparation, and sequencing controls; and computational considerations such as identification of contamination, accounting for uneven sequencing depth, constructing diversity metrics, assigning taxonomy, differential abundance testing, and, finally, data availability. In addition to general considerations, we highlight some special considerations by species and sample type.

Influence of market type and time of purchase on bacterial counts and Salmonella and Listeria prevalence in chicken in Vietnam

The objective of the current study was to determine the influence of market type and sampling time on Salmonella and Listeria prevalence and bacterial counts of 180 whole chicken carcasses collected in 6 supermarkets (SM), 6 indoor markets (IM), and 6 open markets (OM) in Vietnam, at opening (T0) and 4 h after the opening (T4). Salmonella and Listeria prevalence were at least 30.4 and 56.6%, respectively. Chicken carcasses had more than 10.1, 7.5, and 9.4 log CFU/g of aerobic bacteria, Escherichia coli(E. coli), and coliforms, respectively. Both E. coli and coliform counts were greater in IM than in SM (P = 0.002 and 0.006). However, only E. coli counts differed between SM (7.7 log CFU/g) and OM (8.3 log CFU/g; P = 0.024). Whole birds in IM had greater Salmonellaprevalence than birds from both SM and OM by 28.4 and 23.0% (P = 0.006 and 0.022, respectively). Listeria prevalence was less in SM, at 56.6%, than in IM and OM (78.6 and 73.2%, P = 0.024 and 0.089, respectively). These results highlighted high levels of bacteria and high incidence of Salmonella and Listeria in whole chicken in retail establishments in Vietnam, posing potential food safety and public health risks.

Application of Peroxyacetic Acid for Decontamination of Raw Poultry Products and Comparison to Other Commonly Used Chemical Antimicrobial Interventions: A Review

ABSTRACT

Poultry remains one of the top food commodities responsible for foodborne illness in the United States, despite poultry industry efforts since the inception of hazard analysis and critical control point to reduce the burden of foodborne illness implicating poultry products. The appropriate use of antimicrobial compounds during processing of raw poultry can help minimize this risk. Currently, peroxyacetic acid (PAA) is the most popular antimicrobial in the poultry industry, displacing chlorine compounds and others. The aim of this review was to compare the effectiveness of PAA to that of other antimicrobials for the decontamination of raw poultry carcasses and parts. Twenty-six articles were found that compared PAA with over 20 different antimicrobials, applied as spray or immersion treatments for different exposure times and at different concentrations. The most common comparisons were to chlorine compounds (17 articles), to lactic acid compounds (five articles), and to cetylpyridinium chloride (six articles). Studies measured effectiveness by reductions in native flora or inoculated bacteria, usually Salmonella or Campylobacter. PAA was found to be more effective than chlorine under most conditions studied. Effectiveness of PAA was higher than or comparable to that of lactic acid compounds and cetylpyridinium chloride depending on product and treatment conditions. Overall, the results of primary literature studies support the popularity of PAA as an effective intervention against pathogenic bacteria during poultry processing.

HIGHLIGHTS

Select Phytochemicals Reduce Campylobacter jejuni in Postharvest Poultry and Modulate the Virulence Attributes of C. jejuni

Consumption or handling of poultry and poultry products contaminated with Campylobacter species are a leading cause of foodborne illness in humans. Current strategies employed to reduce Campylobacter in live chickens provide inconsistent results indicating the need for an alternative approach. This study investigated the efficacy of phytochemicals, namely, turmeric, curcumin, allyl sulfide, garlic oil, and ginger oil, to reduce Campylobacter jejuni in postharvest poultry and sought to delineate the underlying mechanisms of action. Two experiments were conducted on the thigh skin of the chicken, and each experiment was repeated twice. Samples were inoculated with 50 μl (∼10⁷ CFU/sample) of C. jejuni strain S-8 and allowed to adhere for 30 min. Skin samples were dipped into their respective prechilled treatment solutions (0.25 and 0.5% in experiments 1 and 2, respectively) at 4°C for an hour to simulate chilling tank treatment, followed by plating to enumerate C. jejuni (n = 3 samples/treatment/trial). The mechanisms of action(s) were investigated using subinhibitory concentration (SIC) in adhesion, quorum sensing, and gene expression analyses. Adhesion assay was conducted on the monolayers of ATCC CRL-1590 chicken embryo cells challenged with C. jejuni and incubated in the presence or absence of phytochemicals for 1.5 h, followed by plating to enumerate adhered C. jejuni. The effects of phytochemicals on quorum sensing and cell viability were investigated using Vibrio harveyi bioluminescence and LIVE/Dead BacLight^TM bacterial viability assays, respectively. In addition, droplet digital PCR determined the gene expression analyses of C. jejuni exposed to phytochemicals. Data were analyzed by GraphPad Prism version 9. C. jejuni counts were reduced by 1.0–1.5 Log CFU/sample with garlic oil or ginger oil at 0.25 and 0.5% (p < 0.05). The selected phytochemicals (except curcumin) reduced the adhesion of C. jejuni to chicken embryo cells (p < 0.05). In addition, all the phytochemicals at SIC reduced quorum sensing of C. jejuni (p < 0.05). The cell viability test revealed that cells treated with 0.25% of phytochemicals had compromised cell membranes indicating this as a mechanism that phytochemicals use to damage/kill C. jejuni. This study supports that the application of phytochemicals in postharvest poultry would significantly reduce C. jejuni in poultry meat.

Investigation of microbial contamination in a chicken slaughterhouse environment

The environment in poultry abattoirs is the primary potential source of bacterial contamination and cross-contamination of broiler carcasses. In this context, we explored the influence of chilling water and contact surfaces on the microbial diversity of broiler carcasses in warm and cold seasons. High-throughput sequencing was used to target the V3-V4 region of the 16S rRNA gene. Proteobacteria was the main phylum detected in broiler carcasses and on contact surfaces, whereas Bacteroidetes and Firmicutes had high abundances of the prechilling water in both seasons. At the genus level, Psychrobacter and Acinetobacter were much more abundant on broiler carcasses in the warm season, while Flavobacterium and Psychrobacter dominated in the cold season. LEfSe analysis showed that the chilling tank was a key location where carcass contamination occurred. Therefore, the risk of carcass contamination can be reduced by improving sanitary conditions during processing, installing longer chilling tanks, or increasing the water exchange rate in chilling tanks. The results of this study may be useful for better slaughterhouse environmental hygiene management in different seasons. PRACTICAL APPLICATION: This study will help poultry processing managers better understand the impact of different seasons on the environmental microbiota in the environment and their abundance in poultry processing plants, thus allowing them to adopt proper disinfection strategies for different seasons and environments, further improving the safety and shelf life of products.

The changing microbiome of poultry meat; from farm to fridge

Chickens play host to a diverse community of microorganisms which constitute the microflora of the live bird. Factors such as diet, genetics and immune system activity affect this complex population within the bird, while external influences including weather and exposure to other animals alter the development of the microbiome. Bacteria from these settings including Campylobacter and Salmonella play an important role in the quality and safety of end-products from these birds. Further steps, including washing and chilling, within the production cycle aim to control the proliferation of these microbes as well as those which cause product spoilage. These steps impose specific selective pressures upon the microflora of the meat product. Within the next decade, it is forecast that poultry meat, particularly chicken will become the most consumed meat globally. However, as poultry meat is a frequently cited reservoir of zoonotic disease, understanding the development of its microflora is key to controlling the proliferation of important spoilage and pathogenic bacterial groups present on the bird. Whilst several excellent reviews exist detailing the microbiome of poultry during primary production, others focus on fate of important poultry pathogens such as Campylobacter and Salmonella spp. At farm and retail level, and yet others describe the evolution of spoilage microbes during spoilage. This review seeks to provide the poultry industry and research scientists unfamiliar with food technology process with a holistic overview of the key changes to the microflora of broiler chickens at each stage of the production and retail cycle.

Evaluation of Immersion and Spray Applications of Antimicrobial Treatments for Reduction of Campylobacter jejuni on Chicken Wings

The decontamination efficacy of antimicrobial treatments against Campylobacter jejuni on chicken wings was evaluated. Chicken wings surface-inoculated with C. jejuni (3.9 log colony-forming units [CFU]/mL) were left untreated (control) or were treated by immersion (5 s) or in a spray cabinet (4 s) with water, a sulfuric acid and sodium sulfate blend (SSS; pH 1.2), formic acid (1.5%), peroxyacetic acid (PAA; 550 ppm), or PAA (550 ppm) that was pH-adjusted (acidified) with SSS (pH 1.2) or formic acid (1.5%). All evaluated immersion and spray chemical treatments effectively (p < 0.05) lowered C. jejuni populations on chicken wings. Spray application of chemical treatments resulted in immediate pathogen reductions ranging from 0.5 to 1.2 log CFU/mL, whereas their application by immersion lowered initial pathogen levels by 1.7 to 2.2 log CFU/mL. The PAA and acidified PAA treatments were equally (p ≥ 0.05) effective at reducing initial C. jejuni populations, however, following a 24 h refrigerated (4 °C) storage period, wings treated with acidified PAA had lower (p < 0.05) pathogen levels than samples that had been treated with PAA that was not acidified. Findings of this study should be useful to the poultry industry in its efforts to control Campylobacter contamination on chicken parts.

Microbiota of Chicken Breast and Thigh Fillets Stored under Different Refrigeration Temperatures Assessed by Next-Generation Sequencing

Chicken is one of the most widely consumed meats worldwide. The exploration of the bacterial diversity of chicken meat may provide new insights into the chicken-associated microbiome that will lead to moderation of food spoilage or safety. This study was undertaken to explore the bacterial communities of chicken breast and thigh fillets stored at refrigeration (0 °C and 5 °C) and slightly abuse (10 °C) temperatures for 5 days through conventional cultural methods along with next-generation sequencing (NGS) analysis. Total viable counts (TVC), Brochothrix thermosphacta, Pseudomonas spp., and lactic acid bacteria (LAB) were enumerated, while the bacterial communities were mapped through 16S rRNA gene amplicon sequencing. Chicken breast and thigh fillets possessed a complex bacterial structure that incorporated a total of >200 Operational Taxonomic Units (OTUs) at the genus level. The core microbiota of fresh samples consisted of Acinetobacter, Brochothrix, Flavobacterium, Pseudomonas, Psychrobacter, and Vibrionaceae (family). These genera persisted until the end of storage in >80% of samples, except Psychrobacter and Flavobacterium, while Photobacterium was also identified. Hierarchical clustering showed a distinction of samples based on storage time and chicken part. Conventional plate counting with growth media commonly used in spoilage studies did not always correspond to the microbial community profiles derived from NGS analysis, especially in Pseudomonas, Acinetobacter, Photobacterium, and Vibrionaceae. Results of the present study highlight Photobacterium and Vibrionaceae, in general, as potent chicken meat spoilers and suggest the necessity to combine classical microbiological methods along with NGS technologies to characterize chicken meat spoilage microbiota.

Survival and Control of Campylobacter in Poultry Production Environment

Campylobacter species are Gram-negative, motile, and non-spore-forming bacteria with a unique helical shape that changes to filamentous or coccoid as an adaptive response to environmental stresses. The relatively small genome (1.6 Mbp) of Campylobacter with unique cellular and molecular physiology is only understood to a limited extent. The overall strict requirement of this fastidious microorganism to be either isolated or cultivated in the laboratory settings make itself to appear as a weak survivor and/or an easy target to be inactivated in the surrounding environment of poultry farms, such as soil, water source, dust, surfaces and air. The survival of this obligate microaerobic bacterium from poultry farms to slaughterhouses and the final poultry products indicates that Campylobacter has several adaptive responses and/or environmental niches throughout the poultry production chain. Many of these adaptive responses remain puzzles. No single control method is yet known to fully address Campylobacter contamination in the poultry industry and new intervention strategies are required. The aim of this review article is to discuss the transmission, survival, and adaptation of Campylobacter species in the poultry production environments. Some approved and novel control methods against Campylobacter species throughout the poultry production chain will also be discussed.

Management Strategies for Prevention of Campylobacter Infections Through the Poultry Food Chain: A European Perspective

Numerous studies point out that at present, a complete elimination of Campylobacter species in the poultry food chain is not feasible. Thus, the current aim should be to establish control measures and intervention strategies to minimize the occurrence of Campylobacter spp. in livestock (esp. poultry flocks) and to reduce the quantitative Campylobacter burden along the food chain in animals and subsequently in foods. The most effective measures to mitigate Campylobacter focus on the primary production stage. Nevertheless, measures applied during slaughter and processing complement the general meat hygiene approaches by reducing fecal contamination during slaughtering and processing and as a consequence help to reduce Campylobacter in poultry meat. Such intervention measures at slaughter and processing level would include general hygienic improvements, technological innovations and/or decontamination measures that are applied at single slaughter or processing steps. In particular, approaches that do not focus on a single intervention measure would need to be based on a thorough process of evaluation, and potential combinatory effects have to be modeled and tested. Finally, the education of all stakeholders (including retailers, food handlers and consumers) is required and will help to increase awareness for the presence of foodborne pathogens in raw meat and meat products and can thus aid in the development of the required good kitchen hygiene.

Strategies to Improve Poultry Food Safety, a Landscape Review

Food safety remains a significant public health issue for the poultry industry. Foodborne pathogens can be in contact at all phases of poultry production, from initial hatch to processing and ultimately to retail and meal preparation. Salmonella and Campylobacter have been considered the primary foodborne pathogens associated with poultry. Both organisms are major causative agents of human foodborne illness. Limiting these pathogens in poultry production requires identifying their sources and routes of transmission. This involves the ability to isolate and precisely identify them using methodologies capable of discernment at the genome level. Interventions to reduce their occurrence in poultry production employ two basic strategies: prevention of establishment and elimination of already-established pathogens. This review provides an overview of current findings and prospects for further research on poultry food safety issues.

Active Packaging of Immobilized Zinc Oxide Nanoparticles Controls Campylobacter jejuni in Raw Chicken Meat

Zinc oxide nanoparticles (ZnO NPs) are regarded as a safe and stable antimicrobial that can inactivate bacteria by several potential working mechanisms. We aimed to incorporate ZnO NPs into packaging material to control Campylobacter in raw chicken meat. ZnO NPs were first incorporated into three-dimensional (3D) paper tubes to identify the lethal concentration against Campylobacter jejuni, which was selected as the working concentration to develop 2D functionalized absorbing pads by an ultrasound-assisted dipping technique. The functionalized pad was placed underneath raw chicken meat to inactivate C. jejuni and the predominant chicken microbiota at 4°C within 8 days of storage. Immobilized ZnO NPs at 0.856 mg/cm² reduced C. jejuni from ∼4 log CFU/25 g raw chicken meat to an undetectable level after 3 days of storage. Analysis by inductively coupled plasma-optical emission spectroscopy showed that the Zn level increased from 0.02 to 0.17 mg/cm² in treated raw chicken meat. Scanning electron microscopy validated the absence of nanoparticle migration onto raw chicken meat after treatment. Inactivation of C. jejuni was associated with the increase of lactic acid produced by Lactobacillus in raw chicken meat in a pH-dependent manner. Less than 5% of Zn²⁺ was released from ZnO NPs at neutral pH, while up to 88% was released when the pH was <3.5 within 2 days. Whole-transcriptome sequencing (RNA-Seq) analysis demonstrated a broad effect of ZnO NPs on genes involved in various cellular developmental processes as annotated by gene ontology. Taken together, the results indicate that functionalized absorbing pads inactivated C. jejuni in raw chicken meat by immobilized ZnO NPs along with the controllable released Zn²⁺ IMPORTANCE Prevalence of Campylobacter in raw poultry remains a major food microbiological safety challenge. Novel mitigation strategies are required to ensure the safety and quality of poultry products. Active food packaging can control pathogens without directly adding antimicrobials into the food matrix and extend the food's shelf life. The functionalized absorbing pad with ZnO NPs developed in this study was able to inactivate C. jejuni in raw chicken meat and keep the meat free from C. jejuni contamination during shelf life without any observed migration of nanoparticles. The controllable conversion of immobilized ZnO NPs to free Zn²⁺ makes this approach safe and eco-friendly and paves the way for developing a novel intervention strategy for other high-risk foods. Our study applied nanotechnology to exploit an effective approach for Campylobacter control in raw chicken meat products.

Environmental Influences of High-Density Agricultural Animal Operation on Human Forearm Skin Microflora

The human forearm skin microbiome ecosystem contains rich and diverse microbes, which are influenced by environmental exposures. The microbial representatives can be exchanged between human and environment, specifically animals, by which they share certain or similar epidermal microbes. Livestock and poultry are the microbial sources that are associated with the transmission of community-based pathogenic infections. Here, in this study, we proposed investigating the environmental influences introduced by livestock/poultry operations on forearm skin microflora of on-site farm workers. A total of 30 human skin swab samples were collected from 20 animal workers in dairy or integrated farms and 10 healthy volunteer controls. The skin microbiome was 16S metagenomics that were sequenced with Illumina MiSeq system. For skin microbial community analysis, the abundance of major phyla and genera as well as alpha and beta diversities were compared across groups. We identified distinctive microbial compositional patterns on skin of workers in farm with different animal commodities. Workers in integrated farms containing various animals were associated with higher abundances of epidermal Proteobacteria, especially Pseudomonas and Acinetobacter, but lower Actinobacteria, especially Corynebacterium and Propionibacterium. For those workers with frequent dairy cattle operations, their Firmicutes in the forearm skin microbiota were enriched. Furthermore, farm animal operations also reduced Staphylococcus and Streptococcus, as well as modulated the microbial biodiversity in farm workers' skin microbiome. The alterations of forearm skin microflora in farm workers, influenced by their frequent farm animal operations, may increase their risk in skin infections with unusual pathogens and epidermal diseases.

Application of Amplon in combination with peroxyacetic acid for the reduction of nalidixic acid-resistant Salmonella Typhimurium and Salmonella Reading on skin-on, bone-in tom turkey drumsticks

Peroxyacetic acid (PAA) has become an important component of pathogen reduction in poultry processing, but there are potential concerns for continued exposure. The objective was to evaluate the effects of PAA and Amplon (AMP) used alone or in the combination. Bone-in tom turkey drumsticks (N = 100, n = 10, k = 5, 0 and 24 h) per study were obtained and inoculated with either nalidixic acid–resistant Salmonella Typhimurium or Salmonella Reading (64 μg/mL). The inocula were allowed to adhere to the drums at 4°C for 60 min for a final attachment of 10⁸ and 10⁷ cfu/g per S. Typhimurium and S. Reading, respectively. Drumsticks were treated with a no-treatment control; tap water, pH 8.5 (TW); TW+500 ppm PAA, pH 3.5 (PAA); TW+500 ppm AMP, pH 1.3 (AMP); TW + PAA + AMP (PAA + AMP). Treatments were applied as short duration dips (30 s) and allowed to drip for 2 min. After treatment, drums were stored at 4°C until microbial analyses at 0 and 24 h. Drums were rinsed in neutralizing buffered peptone water and spot plated for total aerobes and Salmonella. Bacterial counts were log₁₀ transformed and analyzed using n-way ANOVA. All treatments reduced S. Reading on turkey legs at both 0 and 24 h (P < 0.0001; P < 0.0001). At 24 h, drums treated with PAA + AMP (3.92 log₁₀ cfu/g) had less S. Reading than no-treatment control, TW, and AMP. Treatment by time interactions were observed for total aerobes among drums in both studies (P < 0.0001, P < 0.0001) and Salmonella among drums inoculated with S. Typhimurium (P < 0.0001). During the S. Reading and S. Typhimurium study, all treatments reduced Salmonella and total aerobes on drums. During the S. Typhimurium study, drums treated with PAA + AMP had the lowest numerical load of S. Typhimurium and total aerobes. The combination of AMP + PAA may exhibit a synergistic effect in reducing Salmonella on turkey drums, thus increasing the safety of turkey products for consumers.

Prevalence of Salmonella enterica on poultry processing equipment after completion of sanitization procedures

Salmonella is a poultry-borne pathogen that causes illness throughout the world. Consequently, it is critical to control Salmonella during the process of converting broilers to poultry meat. Sanitization of a poultry processing facility, including processing equipment, is a crucial control measure that is utilized by poultry integrators. However, prevalence of Salmonella on equipment after sanitization and its potential risk to food safety has not been evaluated thoroughly. Therefore, the objective of this study was to evaluate the persistence of Salmonella on poultry processing equipment before and following cleaning and sanitization procedure. A total of 15 locations within 6 commercial processing plants were sampled at 3 time points: (A) after processing; (B) after cleaning; and (C) after sanitization, on 3 separate visits for a total of 135 samples per plant. Salmonella-positive isolates were recovered from samples using the United States Department of Agriculture MLG 4.09 conventional method. Presumptive Salmonella colonies were subjected to biochemical tests for confirmation. Salmonella isolates recovered after sanitization were serotyped and tested for the presence of specific virulence genes. A completely randomized design with a 6 × 3 × 15 factorial arrangement was utilized to analyze the results for Salmonella prevalence between processing plants. Means were separated using Fishers protected least significant difference when P ≤ 0.05. For Salmonella prevalence between processing plants, differences (P < 0.0001) were observed in the 6 plants tested where the maximum and minimum prevalence was 29.6 and 7.4%, respectively. As expected, there was a difference (P < 0.0001) in the recovery of Salmonella because of sampling time. Salmonella prevalence at time A (36%) was significantly higher, whereas there was no difference between time B (12%) and C (9%). There was a location effect (P < 0.0001) for the prevalence of Salmonella with the head puller, picker, cropper, and scalder having a significantly higher prevalence when compared with several other locations. At sampling time C, a trend toward a difference (P = 0.0899) was observed for Salmonella prevalence between the 6 plants, whereas significant differences were observed because of location (P = 0.0031). Five prominent Salmonella enterica serovars were identified, including Kentucky, Schwarzengrund, Enteritidis, Liverpool, and Typhimurium with S. Kentucky being the most prevalent. PCR analysis of 8 Salmonella virulence genes showed that the invA, sipB, spiA, sseC, and fimA were detected in all isolates, whereas genes carried on plasmids and/or fimbriae varied remarkably among all isolates. This study established Salmonella prevalence and persistence in poultry processing facilities after antimicrobial application through sanitization procedures which could result in contamination of poultry carcasses and food safety risks because of poultry meat.

Antimicrobial resistance associated with the use of antimicrobial processing aids during poultry processing operations: cause for concern?

Antimicrobial resistance has become a global issue and a threat to human and animal health. Contamination of poultry carcasses with meat-borne pathogens represents both an economic and a public health concern. The use of antimicrobial processing aids (APA) during poultry processing has contributed to an improvement in the microbiological quality of poultry carcasses. However, the extensive use of these decontaminants has raised concerns about their possible role in the co-selection of antibiotic-resistant bacteria. This topic is presented in the current review to provide an update on the information related to bacterial adaptation to APA used in poultry processing establishments, and to discuss the relationship between APA bacterial adaptation and the acquisition of a new resistance phenotype to therapeutic antimicrobials by bacteria. Common mechanisms such as active efflux and changes in membrane fluidity are the most documented mechanisms responsible for bacterial cross-resistance to APA and antimicrobials. Although most studies reported a bacterial resistance to antibiotics not reaching a clinical level, the under-exposure of bacteria to APA remains a concern in the poultry industry. Further research is needed to determine if APA used during poultry processing and therapeutic antimicrobials share common sites of action in bacteria and encounter similar mechanisms of resistance.

A Review of Salmonella and Campylobacter in Broiler Meat: Emerging Challenges and Food Safety Measures

Poultry is one of the largest sources of animal-based protein in the United States. Poultry processing has grown from a small local network of plants to nearly 500 plants nationwide. Two of the most persistent bacteria in poultry processing are Salmonella and Campylobacter. It was not until the introduction of Hazard Analysis and Critical Control Point systems in 1996 that major efforts to reduce bacterial contamination were developed. Traditionally, chlorine has been the industry standard for decontaminating chicken meat. However, antimicrobials such as peracetic acid, cetylpyridinium chloride, and acidified sodium chlorite have replaced chlorine as primary antimicrobials. Despite current interventions, the emergence of stress-tolerant and biofilm-forming Salmonella and Campylobacter is of primary concern. In an effort to offset growing tolerance from microbes, novel techniques such as cold plasma treatment, electrostatic spraying, and bacteriophage-based applications have been investigated as alternatives to conventional treatments, while new chemical antimicrobials such as Amplon and sodium ferrate are investigated as well. This review provides an overview of poultry processing in the United States, major microbes in poultry processing, current interventions, emerging issues, and emerging technologies in antimicrobial treatments.

Impact of Poultry Processing Operating Parameters on Bacterial Transmission and Persistence on Chicken Carcasses and Their Shelf Life

It is important for the poultry industry to maximize product safety and quality by understanding the connection between bacterial diversity on chicken carcasses throughout poultry processing to the end of shelf life and the impact of the local processing environment. Enumeration of total aerobic bacteria, Campylobacter and Pseudomonas, and 16S rRNA gene amplicon sequencing were used to evaluate the processing line by collecting 10 carcasses from five processing steps: prescald, postplucker, pre- and post-immersion chill, and post-air chill. The diversity throughout a 12-day shelf life was also determined by examining 30 packaged carcasses. To identify the sources of possible contamination, scald water tank, immersion chilling water tank, air samples, and wall surfaces in the air-chill room were analyzed. Despite bacterial reductions on carcasses (>5 log10 CFU/ml) throughout the process, each step altered the bacterial diversity. Campylobacter was a minor but persistent component in the bacterial community on carcasses. The combination of scalding, defeathering, and plucking distributed thermophilic spore-forming Anoxybacillus to carcasses, which remained at a high abundance on carcasses throughout subsequent processes. Pseudomonas was not isolated from carcasses after air chilling but was abundant on the wall of the air-chill room and became the predominant taxon at the end of shelf life, suggesting possible contamination through air movement. The results suggest that attention is needed at each processing step, regardless of bacterial reductions on carcasses. Changing scalding water regularly, maintaining good hygiene practices during processing, and thorough disinfection at the end of each processing day are important to minimize bacterial transmission.IMPORTANCE Culture-based and culture-independent approaches were utilized to reveal bacterial community changes on chicken carcasses at different processing steps and potential routes from the local processing environment. Current commercial processing effectively reduced bacterial loads on carcasses. Poultry processes have similar processes across facilities, but various processing arrangements and operating parameters could impact the bacterial transmission and persistence on carcasses differently. This study showed the use of a single tunnel incorporating scalding, defeathering and plucking may undesirably distribute the thermoduric bacteria, e.g., Campylobacter and Anoxybacillus, between the local environment and carcasses, whereas this does not occur when these steps are separated. The length of immersion and air chilling also impacted bacterial diversity on carcasses. Air chilling can transfer Pseudomonas from wall surfaces onto carcasses; this may subsequently influence chicken product shelf life. This study helps poultry processors understand the impact of current commercial processing and improve the chicken product quality and safety.

Efficacy of peroxy acetic acid in reducing Salmonella and Campylobacter spp. populations on chicken breast fillets

Poultry processors use antimicrobials to reduce the risk of pathogens on poultry and poultry products. The efficacy of selective and nonselective plating media to enumerate injured Salmonella (selective media-brilliant green sulfa agar and Petrifilm Enterobacteriaceae Plate Count; nonselective media-tryptic soy agar and Petrifilm Aerobic Plate Count) and Campylobacter (selective medium-Campy cefex agar and nonselective medium-Brucella agar) populations and the efficacy of peroxy acetic acid (PAA) to reduce Salmonella and Campylobacter populations on chicken breast fillets were evaluated. All plating media for Salmonella and Campylobacter contained nalidixic acid (200 ppm) or gentamycin (200 ppm), respectively. Breast fillets were sprayed or immersed in PAA (500 ppm) for 10 min for evaluation of the plating media. Breast fillets inoculated with a mixed Salmonella and Campylobacter cocktail were sprayed (5 or 10 s) or immersed (4-30 s) in PAA (100, 400, 500, or 1,000 ppm) for evaluation of PAA efficacy. Salmonella populations were higher (P ≤ 0.05) when plated on nonselective media compared with the selective media for the non-PAA treated fillets, although the differences in populations were low (<0.32 log CFU/mL). For both the microorganisms, populations on PAA treated (immersion or spray) fillets were similar when enumerated on nonselective or selective media within each treatment (PAA immersion or spray). Both immersion and spray applications reduced (P ≤ 0.05) the Salmonella and Campylobacter populations compared with the control. Increasing the PAA concentration to 250, 500, and 1,000 ppm resulted in greater reductions (P ≤ 0.05) in Salmonella and Campylobacter populations. Immersion of the inoculated breast fillets in 1,000 ppm PAA solution for 30 s resulted in Salmonella and Campylobacter population reductions of 1.92 and 1.87 log CFU/mL, respectively. Method of antimicrobial application (immersion and spray) did not affect the reductions in Salmonella and Campylobacter populations. Either immersion or spray application can be used to improve microbial safety of chicken breast fillets in a poultry processing plant.

Poultry processing and the application of microbiome mapping

Chicken is globally one of the most popular food animals. However, it is also one of the major reservoirs for foodborne pathogens, annually resulting in continued morbidity and mortality incidences worldwide. In an effort to reduce the threat of foodborne disease, the poultry industry has implemented a multifaceted antimicrobial program that incorporates not only chemical compounds, but also extensive amounts of water application and pathogen monitoring. Unfortunately, the pathogen detection methods currently used by the poultry industry lack speed, relying on microbiological plate methods and molecular detection systems that take time and lack precision. In many cases, the time to data acquisition can take 12 to 24 h. This is problematic if shorter-term answers are required which is becoming more likely as the public demand for chicken meat is only increasing, leading to new pressures to increase line speed. Therefore, new innovations in detection methods must occur to mitigate the risk of foodborne pathogens that could result from faster slaughter and processing speeds. Future technology will have 2 tracks: rapid methods that are meant to detect pathogens and indicator organisms within a few hours, and long-term methods that use microbiome mapping to evaluate sanitation and antimicrobial efficacy. Together, these methods will provide rapid, comprehensive data capable of being applied in both risk-assessment algorithms and used by management to safeguard the public.

Mealworm larvae (Tenebrio molitor L.) exuviae as a novel prebiotic material for BALB/c mouse gut microbiota

The objective of this study was to evaluate the effect of yellow mealworm (Tenebrio molitor L.) exuviae (ME) given as a prebiotic in 20% of the diet fed to BALB/c mice. Analysis of the ME revealed that it was mostly composed of crude protein (52.94%), crude fiber (10.70%), and moisture (10.54%). When ME was fed to mice for 8 weeks, the number of intestinal lactic acid bacteria increased, reaching similar numbers (4.50 ± 0.80 CFU/mL) to those (4.70 ± 0.80 CFU/mL) of the control group not fed ME. Microbiome analysis showed that 8 weeks feeding of ME promoted the growth of Bifidobacteriaceae and Lactobacillaceae compared to the POS group, indicating the positive effects of feeding 20% ME on the intestinal microbiota of mice. These results suggest that ME can be considered as a dietary prebiotics to improve human gut microbial population, but further application study to human is necessary.

A Microbiomic Analysis of a Pasture-Raised Broiler Flock Elucidates Foodborne Pathogen Ecology Along the Farm-To-Fork Continuum

While conventionally grown poultry continues to dominate the U. S. poultry industry, there is an increasing demand for locally-grown, "all natural" alternatives. The use of next generation sequencing allows for not only the gross (e.g., community structure) but also fine-scale (e.g., taxa abundances) examination of these complex microbial communities. This data provides a better understanding of how a pasture flock's microbiome changes throughout the production life cycle and how that change in microbial ecology changes foodborne pathogens in alternative poultry production systems. In order to understand this ecology better, pooled broiler samples were taken during the entire flock life cycle, from pre-hatch gastrointestinal samples (N = 12) to fecal samples from the brood (N = 5), and pasture (N = 10) periods. Additional samples were taken during processing, including skin and feather rinsates (N = 12), ceca (N = 12), and whole carcass rinses (N = 12), and finally whole carcasss rinsates of final products (N = 3). Genomic DNA was extracted, 16S rDNA microbiome sequencing was conducted (Illumina MiSeq), and microbiomes were analyzed and compared using QIIME 1.9.1 to determine how microbiomes shifted throughout production continuum, as well as what environmental factors may be influencing these shifts. Significant microbiome shifts occurred during the life cycle of the pasture broiler flock, with the brood and pasture fecal samples and cecal samples being very distinct from the other pre-hatch, processing, and final product samples. Throughout these varied microbiomes, there was a stable core microbiome containing 13 taxa. Within this core microbiome, five taxa represented known foodborne pathogens (Salmonella, Campylobacter) or potential/emerging pathogens (Pseudomonas, Enterococcus, Acinetobacter) whose relative abundances varied throughout the farm-to-fork continuum, although all were more prevalent in the fecal samples. Additionally, of the 25 physiochemical and nutrient variables measured from the fecal samples, the carbon to nitrogen ratio was one of the most significant variables to warrant further investigations because it impacted both general fecal microbial ecology and Campylobacter and Enterococcus taxa within the core fecal microbiomes. These findings demonstrate the need for further longitudinal, farm-to-fork studies to understand the ecology of the microbial ecology of pasture production flocks to improve animal, environmental, and public health.

Microbiota Analysis for the Optimization of Campylobacter Isolation From Chicken Carcasses Using Selective Media

Since contaminated poultry meat is the major source of transmitting Campylobacter jejuni to humans, the isolation of Campylobacter from poultry carcasses is frequently performed in many countries as a baseline survey to ensure food safety. However, existing isolation methods have technical limitations in isolating this fastidious bacterium, such as a growth competition with indigenous bacteria in food samples. In this study, we compared the differences in microbiota compositions between Bolton and Preston selective media, two most common selective media to isolate Campylobacter, and investigated how different microbiota compositions resulting from different enrichment methods may affect isolation frequencies. A next-generation sequencing (NGS) analysis of 16S rRNA demonstrated that Bolton and Preston-selective enrichments generated different microbiota structures that shared only 31.57% of Operating Taxonomic Unit (OTU) types. Particularly, Escherichia was highly prevalent in Bolton selective media, and the enrichment cultures that increase Escherichia negatively affected the efficacy of Campylobacter isolation. Furthermore, the combination of the selective media made a significant difference in the isolation frequency. The Bolton broth and Preston agar combination exhibited the highest (60.0%) frequencies of Campylobacter isolation, whereas the Bolton broth and Bolton agar combination showed the lowest (2.5%). These results show that each selective medium generates a unique microbiota structure and that the sequence of combining the selective media also critically affects the isolation frequency by altering microbiota compositions. In this study, we demonstrated how a microbiota analysis using NGS can be utilized to optimize a protocol for bacterial isolation from food samples.

Comparison of 16S rDNA Next Sequencing of Microbiome Communities From Post-scalder and Post-picker Stages in Three Different Commercial Poultry Plants Processing Three Classes of Broilers

Poultry processing systems are a complex network of equipment and automation systems that require a proactive approach to monitoring in order to protect the food supply. Process oversight requires the use of multi-hurdle intervention systems to ensure that any undesirable microorganisms are reduced or eliminated by the time the carcasses are processed into final products. In the present study, whole bird carcass rinses (WBCR) collected at the post-scalder and post-picker locations from three different poultry processing facilities (Plant A: mid-weight broiler processing, B: large-weight broiler processing, C: young broiler (Cornish) processing) were subjected to next generation sequencing (NGS) and microbial quantification using direct plating methods to assess the microbial populations present during these stages of the poultry process. The quantification of aerobic plate counts (APC) and Enterobacteriaceae (EB) demonstrated that reductions for these microbial classes were not consistent between the two sampling locations for all facilities, but did not provide a clear picture of what microorganism(s) may be affecting those shifts. With the utilization of NGS, a more complete characterization of the microbial communities present including microorganisms that would not have been identified with the employed direct plating methodologies were identified. Although the foodborne pathogens typically associated with raw poultry, Salmonella and Campylobacter, were not identified, sequence analysis performed by Quantitative Insights of Microbiology Ecology (QIIME) indicated shifts of Erwinia, Serratia, and Arcobacter, which are microorganisms closely related to Salmonella and Campylobacter. Additionally, the presence of Chryseobacterium and Pseudomonas at both sampling locations and at all three facilities provides evidence that these microorganisms could potentially be utilized to assess the performance of multi-hurdle intervention systems.

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.

Frequent Implication of Multistress-Tolerant Campylobacter jejuni in Human Infections

Campylobacter jejuni, a major cause of bacterial foodborne illnesses, is considered highly susceptible to environmental stresses. In this study, we extensively investigated the stress tolerance of 121 clinical strains of C. jejuni against 5 stress conditions (aerobic stress, disinfectant exposure, freeze-thaw, heat treatment, and osmotic stress) that this pathogenic bacterium might encounter during foodborne transmission to humans. In contrast to our current perception about high stress sensitivity of C. jejuni, a number of clinical strains of C. jejuni were highly tolerant to multiple stresses. We performed population genetics analysis by using comparative genomic fingerprinting and showed that multistress-tolerant strains of C. jejuni constituted distinct clades. The comparative genomic fingerprinting subtypes belonging to multistress-tolerant clades were more frequently implicated in human infections than those in stress-sensitive clades. We identified unique stress-tolerant C. jejuni clones and showed the role of stress tolerance in human campylobacteriosis.