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

Tracking the contamination sources of microbial population and characterizing Listeria monocytogenes in a chicken slaughterhouse by using culture-dependent and -independent methods

Listeria monocytogenes is the etiologic agent of listeriosis, a foodborne disease that poses a threat to public health globally. Chicken meat exhibits heightened susceptibility to L. monocytogenes contamination during butchery. The persistence of this pathogen in the slaughterhouse environment enables recurring contamination of meat products. This study aimed at identifying the sources and transmission routes of L. monocytogenes contamination within an abattoir where it was consistently detected for three consecutive years (2019-2021). Furthermore, the environmental factors aiding contamination along chicken processing lines were determined by surveying the microbiome within the facility. Samples collected in 2019 to 2021 were subjected to culture-dependent analysis to assess the prevalence, serotypes, and multi-locus sequence typing (MLST) of L. monocytogenes. Additionally, the specimens collected in 2021 underwent culture-independent analysis via real-time quantitative polymerase chain reaction (qPCR) and 16S rRNA gene amplicon sequencing to identify the contamination sources and characterize the entire microbial community within the slaughterhouse. L. monocytogenes was isolated only from the clean zone, where the final slaughtering stage occurs. Most strains isolated from the final carcasses showed the same genetic cluster as the isolate in the chilling water and were assigned to MLST profile ST3. Culture-independent qPCR confirmed L. monocytogenes contamination in all samples, excluding post-scalding carcasses, prewashed post-evisceration carcasses, and the bleeding areas. Consequently, qPCR enabled more comprehensive identification of L. monocytogenes contamination points than culture-dependent approaches. Moreover, 16S rRNA gene amplicon sequencing demonstrated that psychro-tolerant and spoilage-related bacteria with L. monocytogenes-like attributes exhibited enhanced viability in the clean zone and immersion-chilling water. Metagenomics-based source tracking analysis further revealed that the shackles and chilling waters represent predominant sources of cross-contamination between different slaughterhouse zones, whereas the grading and packaging workstations and chilling water in the clean zone were deemed crucial sources affecting final carcass contamination. Collectively, these findings demonstrate through culture-dependent and -independent methods that L. monocytogenes spreads along the slaughter line, contaminating the slaughterhouse. Moreover, by investigating changes in microbial community and bacterial flow along the slaughter line within the facility, the sources influencing carcass contamination can be effectively traced.

Characterization of microbial ecology, Listeria monocytogenes, and Salmonella sp. on equipment and utensil surfaces in Brazilian poultry, pork, and dairy industries

This study aimed to evaluate the level of counting by indicator microorganisms, identify the microbial ecology, detect Listeria monocytogenes and Salmonella sp., and determine the presence of virulence genes and biofilm formation. A total of 480 samples were collected from the surfaces of the equipment and utensils using sterile swabs for the detection of L. monocytogenes and Salmonella sp. and counting mesophilic aerobes, Enterobacteriaceae, Escherichia coli, and Pseudomonas sp. The microbial ecology was evaluated by sequencing the 16S rRNA gene. Genes for virulence and biofilm formation were analyzed and adhesion capacity was evaluated for L. monocytogenes and Salmonella sp. The mesophilic aerobe count was the highest in the dairy processing facility, followed by the pork and poultry slaughterhouses. L. monocytogenes was detected in all facilities, with the highest detection in the pork slaughterhouse, followed by the poultry and dairy facilities. Salmonella sp. was only detected in the dairy. Isolates of L. monocytogenes and Salmonella sp. showed poor adhesion to polystyrene surfaces, virulence genes, and biofilm formation. The frequent contaminants in the slaughterhouses were Pseudomonas, Acinetobacter, and Aeromonas in poultry, Acinetobacter, Pseudomonas, and Brevundimonas in pork, and Pseudomonas, Kocuria, and Staphylococcus in dairy. Our results provide useful information to understand the microbiological risks associated with contamination.

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.

Comparative resistome, mobilome, and microbial composition of retail chicken originated from conventional, organic, and antibiotic-free production systems

The aim of this study was to investigate the microbial composition, and the profiles of antimicrobial resistance genes (ARGs, resistome) and mobile genetic elements (mobilome) of retail chicken carcasses originated from conventional intensive production systems (CO), certified antimicrobial-free intensive production systems (AF), and certified organic production systems with restricted antimicrobial use (OR). DNA samples were collected from 72 chicken carcasses according to a cross-sectional study design. Shot-gun metagenomics was performed by means of Illumina high throughput DNA sequencing followed by downstream bioinformatic analyses. Gammaproteobacteria was the most abundant bacterial class in all groups. Although CO, AF, and OR did not differ in terms of alpha- and beta-microbial diversity, the abundance of some taxa differed significantly across the groups, including spoilage-associated organisms such as Pseudomonas and Acinetobacter. The co-resistome comprised 29 ARGs shared by CO, AF and OR, including genes conferring resistance to beta-lactams (blaACT-8, 10, 13, 29; blaOXA-212;blaOXA-275 and ompA), aminoglycosides (aph(3')-IIIa, VI, VIa and spd), tetracyclines (tet KL (W/N/W and M), lincosamides (inu A,C) and fosfomycin (fosA). ARGs were significantly less abundant (P < 0.05) in chicken carcasses from AF and OR compared with CO. Regarding mobile genetic elements (MGEs), transposases accounted for 97.2% of the mapped genes. A higher abundance (P = 0.037) of MGEs was found in CO compared to OR. There were no significant differences in ARGs or MGEs diversity among groups according to the Simpson´s index. In summary, retail frozen chicken carcasses from AF and OR systems show similar ARGs, MGEs and microbiota profiles compared with CO, even though the abundance of ARGs and MGEs was higher in chicken carcasses from CO, probably due to a higher selective pressure.

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.

oprL Gene Sequencing, Resistance Patterns, Virulence Genes, Quorum Sensing and Antibiotic Resistance Genes of XDR Pseudomonas aeruginosa Isolated from Broiler Chickens

Background

Pseudomonas aeruginosa is incriminated in septicemia, significant economic losses in the poultry production sector, and severe respiratory infections in humans. This study aimed to investigate the occurrence, oprL sequencing, antimicrobial resistance patterns, virulence-determinant, Quorum sensing, and antibiotic resistance genes of P. aeruginosa retrieved from broiler chickens.

Methods

Two hundred samples were collected from 120 broiler chickens from broiler farms at Ismailia Governorate, Egypt. Consequently, the bacteriological examination was conducted and the obtained P. aeruginosa strains were tested for oprL gene sequencing, antibiogram, and PCR screening of virulence, Quorum sensing, and antibiotic resistance genes.

Results

The overall prevalence of P. aeruginosa in the examined birds was 28.3%. The oprL gene sequence analysis underlined that the tested strain expressed a notable genetic identity with various P. aeruginosa strains isolated from different geographical areas in the USA, India, China, Chile, and Ghana. PCR evidenced that the obtained P. aeruginosa strains, carrying virulence-related genes: oprL, toxA, aprA, phzM, and exoS in a prevalence of 100%, 100%, 42.5%, 33.3%, and 25.9%, respectively. Moreover, the recovered P. aeruginosa strains possessed the Quorum sensing genes: lasI, lasR, rhlI, and rhlR in a prevalence of 85.2%, 85.2%, 81.5%, and 81.5%, respectively. Furthermore, 40.7% of the isolated P. aeruginosa were XDR to seven antimicrobial classes, possessing sul1, bla _TEM, tetA, bla _CTX-M, bla _OXA-1, and aadA1 genes.

Conclusion

As we can tell, this is the first report emphasizing the evolution of XDR P. aeruginosa strains from broiler chicken in Egypt, which is supposed to be a serious threat to public health. The emerging XDR P. aeruginosa in poultry frequently harbored the oprL, toxA, and aprA virulence genes, the lasI, lasR, rhlI, and rhlR Quorum sensing genes, and the sul1, bla _TEM, tetA, bla _CTXM, bla _OXA-1, and aadA1 resistance genes.

Quantitative Bio-Mapping of Salmonella and Indicator Organisms at Different Stages in a Commercial Pork Processing Facility

The purpose of this study was to develop a quantitative baseline of indicator organisms and Salmonella by bio-mapping throughout the processing chain from harvest to final product stages within a commercial conventional design pork processing establishment. Swab samples were taken on the harvest floor at different processing steps, gambrel table, after polisher, before final rinse, after the final rinse, post snap chill, and after peroxyacetic acid (PAA) application, while 2-pound product samples were collected for trim and ground samples. The samples were subjected to analysis for indicator microorganism enumeration, Aerobic Count (AC), Enterobacteriaceae (EB), and generic Escherichia coli (EC), with the BioMérieux TEMPO®. Salmonella prevalence and enumeration was evaluated using the BAX® System Real-Time Salmonella and the SalQuant™ methodology. Microbial counts were converted to Log Colony-forming units (CFU) on a per mL, per g or per sample basis, presented as LogCFU/mL, LogCFU/g and LogCFU/sample, prior to statistical analysis. All indicator microorganisms were significantly reduced at the harvest floor (p-value < 0.001), from gambrel table to after PAA cabinet location. The reduction at harvest was 2.27, 2.46 and 2.24 LogCFU/mL for AC, EB and EC, respectively. Trim sample values fluctuated based on cut, with the highest average AC count found at neck trim (2.83 LogCFU/g). Further process samples showed the highest AC count in sausage with a mean of 5.28 LogCFU/g. EB counts in sausage (3.19 LogCFU/g) showed an evident increase, compared to the reduction observed at the end of harvest and throughout trim processing. EC counts showed a similar trend to EB counts with the highest value found in sausage links (1.60 LogCFU/g). Statistical microbial process control (SPC) parameters were also developed for each of the indicator microorganisms, using the overall mean count (X=), the Lower control limit (LCL) and Upper control limit (UCL) at each sampling location. For Salmonella prevalence, a total of 125/650 samples were found positive (19%). From those positive samples, 47 samples (38%) were suitable for enumeration using the BAX® System SalQuant™, the majority detected at the gambrel table location. From those enumerable samples, 60% were estimated to be between 0.97 and 1.97 LogCFU/sample, while the rest (40%) were higher within the 2.00−4.02 LogCFU/sample range. This study provides evidence for the application of indicator and pathogen quantification methodologies for food safety management in commercial pork processing operations.

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.

Livestock microbial landscape patterns: Retail poultry microbiomes significantly vary by region and season

Microbes play key roles in animal welfare and food safety but there is little understanding of whether microbiomes associated with livestock vary in space and time. Here we analysed the bacteria associated with the carcasses of the same breed of 28 poultry broiler flocks at different stages of processing across two climatically similar UK regions over two seasons with 16S metabarcode DNA sequencing. Numbers of taxa types did not differ by region, but did by season (P = 1.2 × 10-19), and numbers increased with factory processing, especially in summer. There was also a significant (P < 1 × 10-4) difference in the presences and abundances of taxa types by season, region and factory processing stage, and the signal for seasonal and regional differences remained highly significant on final retail products. This study therefore revealed that both season and region influence the types and abundances of taxa on retail poultry products. That poultry microbiomes differ in space and time should be considered when testing the efficacy of microbial management interventions designed to increase animal welfare and food safety: these may have differential effects on livestock depending on location and timing.

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.

A systematic review from basics to omics on bacteriophage applications in poultry production and processing

The growing human population is currently facing an unprecedented challenge on global food production and sustainability. Despite recognizing poultry as one of the most successful and rapidly growing food industries to address this challenge; poultry health and safety remain major issues that entail immediate attention. Bacterial diseases including colibacillosis, salmonellosis, and necrotic enteritis have become increasingly prevalent during poultry production. Likewise, outbreaks caused by consumption of undercooked poultry products contaminated with zoonotic bacterial pathogens such as Salmonella, Campylobacter and Listeria, are a serious public health concern. With antimicrobial resistance problem and restricted use of antibiotics in food producing animals, bacteriophages are increasingly recognized as an attractive natural antibacterial alternative. Bacteriophages have recently shown promising results to treat diseases in poultry, reduce contamination of carcasses, and enhance the safety of poultry products. Omics technologies have been successfully employed to accurately characterize bacteriophages and their genes/proteins important for interaction with bacterial hosts. In this review, the potential of using lytic bacteriophages to mitigate the risk of major poultry-associated bacterial pathogens are explored. This study also explores challenges associated with the adoption of this technology by industries. Furthermore, the impact of omics approaches on studying bacteriophages, their host interaction and applications is discussed.

Pseudomonas aeruginosa infection of avian origin: Zoonosis and one health implications

Zoonotic diseases are diseases that are transmitted from animals to humans and vice versa. Pseudomonas aeruginosa (P. aeruginosa) is a pathogen with zoonotic nature. Commercial poultry could be infected with P. aeruginosa, especially at young ages with great losses. Infection of embryos with P. aeruginosa induced death in the shell, while infection of chicks led to septicemia, respiratory and enteric infections, and high mortality. Humans are also highly susceptible to P. aeruginosa infection, and the disease is associated with severe lung damage, especially in immunocompromised patients. Chicken carcass and related poultry retail products play an important role in the transmission of P. aeruginosa to humans, especially after processing in abattoirs. Treatment of P. aeruginosa infection is extremely difficult due to continuous development of antibiotic resistance. The transfer of antibiotic-resistant genes from poultry products to humans creates an additional public health problem. Accordingly, this study focused on avian pseudomonad, especially P. aeruginosa, with respect to infection of poultry, transmission to humans, and treatment and antibiotic resistance.

Utilizing the Microbiota and Machine Learning Algorithms To Assess Risk of Salmonella Contamination in Poultry Rinsate

ABSTRACT

Traditional microbiological testing methods are slow, and many molecular-based techniques rely on culture-based enrichment to overcome low limits of detection. Recent advancements in sequencing technologies may make it possible to utilize machine learning to identify patterns in microbiome data to potentially predict the presence or absence of pathogens. In this study, 299 poultry rinsate samples from various points in the processing chain were analyzed to determine if microbiota could inform about a sample's risk for containing Salmonella. Samples were culture confirmed as Salmonella positive or negative following modified U.S. Department of Agriculture Microbiological Laboratory Guidebook protocols. The culture confirmation result was used as a reference to compare with 16S sequencing data. Prechill samples tested positive (71 of 82) at a higher frequency than postchill samples (30 of 217) and contained greater microbial diversity. Due to the larger sample size, postchill samples were analyzed more thoroughly. Analysis of variance identified a significant effect of chilling on the number of genera (P < 0.001), but analysis of similarities failed to provide evidence for microbial dissimilarity between pre- and postchill samples (P = 0.001, R = 0.443). Various machine learning models were trained by using postchill samples to predict if a sample contained Salmonella on the basis of the samples' microbiota preenrichment. The optimal model was a random forest-based model with a performance as follows: accuracy (88%), sensitivity (85%), and specificity (90%). Although the algorithms described in this article are prototypes, these risk-based algorithms demonstrate the potential and need for further studies to provide insight alongside diagnostic tests. Combining risk-based information with diagnostic tools can help poultry processors make informed decisions to help identify and prevent the spread of Salmonella. These data add to the growing body of literature exploring novel ways to utilize microbiome data for predictive food safety.

HIGHLIGHTS

Reduction of Salmonella Infantis on skin-on, bone-in chicken thighs by cetylpyridinium chloride application and the impact on the skin microbiota

Salmonella Infantis has been the etiological agent of numerous foodborne outbreaks of nontyphoidal Salmonella. Consequently, there is an emergent need to mitigate Salmonella Infantis among poultry. Thus, this study evaluated the efficacy of cetylpyridinium chloride (CPC) versus peroxyacetic acid (PAA), on bone-in, skin-on chicken thighs for the reduction of Salmonella and changes in the microbiota. Exactly 100 skin-on, bone-in chicken thighs (2 trials, 0 and 24 h, k = 5, n = 5, N = 50) were inoculated with 10⁸ CFU/mL of a nalidixic acid resistant strain of S. Infantis for an attachment of 10⁶ CFU/g. Thighs were treated with 20 s part dips (350 mL): a no inoculum, no treatment control (NINTC); no treatment control (NTC); tap water (TW); TW+CPC; TW+PAA. Following treatment, thighs were rinsed in 150 mL of nBPW, and rinsates were collected. Rinsates were spot plated for Salmonella and aerobic bacteria (APC). Log₁₀ transformed counts were analyzed using a mixed-effects model (random effect = trial) with means separated using Tukey's HSD (P ≤ 0.05). The genomic DNA of rinsates was extracted, and the 16S rDNA was sequenced on an Illumina MiSeq. Microbiota data were analyzed using QIIME2, with data considered significant at P ≤ 0.05 (main effects) and Q≤0.05 (pairwise differences). Treatment × time interactions were observed for both Salmonella and APC (P < 0.05). The treatment of thighs with PAA and CPC reduced Salmonella and APC in respect to the controls. Numerically, thighs treated with CPC had less Salmonella (4.29 log₁₀CFU/g) and less APC (4.56 log₁₀CFU/g) at 24 h than all other treatments (P > 0.05). Differences in diversity metrics were not consistently observed between treatments; however, in trial 2, the NTC treated thighs were different than those treated with CPC (P < 0.05; Q < 0.05). In both trials, ANCOM, the analysis of microbiome compositional profiles, revealed shifts at both the phylum and order levels with thighs being different in the relative abundances of Proteobacteria (P < 0.05). In conclusion, treatment of skin-on poultry parts with CPC may reduce the risk of foodborne outbreaks caused by Salmonella Infantis.

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.

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.

Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics

The United States' large-scale poultry meat industry is energy and water intensive, and opportunities may exist to improve sustainability during the broiler chilling process. By USDA regulation, after harvest the internal temperature of the chicken must be reduced to 40°F or less within 16 h to inhibit bacterial growth that would otherwise compromise the safety of the product. This step is accomplished most commonly by water immersion chilling in the United States, while air chilling methods dominate other global markets. A comprehensive understanding of the differences between these chilling methods is lacking. Therefore, we assessed the meat quality, shelf-life, microbial ecology, and techno-economic impacts of chilling methods on chicken broilers in a university meat laboratory setting. We discovered that air chilling methods resulted in superior chicken odor and shelf-life, especially prior to 14 days of dark storage. Moreover, we demonstrated that air chilling resulted in a more diverse microbiome that we hypothesize may delay the dominance of the spoilage organism Pseudomonas Finally, a techno-economic analysis highlighted potential economic advantages to air chilling compared to water chilling in facility locations where water costs are a more significant factor than energy costs.IMPORTANCE As the poultry industry works to become more sustainable and to reduce the volume of food waste, it is critical to consider points in the processing system that can be altered to make the process more efficient. In this study, we demonstrate that the method used during chilling (air versus water chilling) influences the final product microbial community, quality, and physiochemistry. Notably, the use of air chilling appears to delay the bloom of Pseudomonas spp. that are the primary spoilers in packaged meat products. By using air chilling to reduce carcass temperatures instead of water chilling, producers may extend the time until spoilage of the products and, depending on the cost of water in the area, may have economic and sustainability advantages. As a next step, a similar experiment should be done in an industrial setting to confirm these results generated in a small-scale university lab facility.

Antibiotic Resistance and Phylogeny of Pseudomonas spp. Isolated over Three Decades from Chicken Meat in the Norwegian Food Chain

Pseudomonas is ubiquitous in nature and a predominant genus in many foods and food processing environments, where it primarily represents major food spoilage organisms. The food chain has also been reported to be a potential reservoir of antibiotic-resistant Pseudomonas. The purpose of the current study was to determine the occurrence of antibiotic resistance in psychrotrophic Pseudomonas spp. collected over a time span of 26 years from retail chicken in Norway and characterize their genetic diversity, phylogenetic distribution and resistance genes through whole-genome sequence analyses. Among the 325 confirmed Pseudomonas spp. isolates by 16S rRNA gene sequencing, antibiotic susceptibility profiles of 175 isolates to 12 antibiotics were determined. A subset of 31 isolates being resistant to ≥3 antibiotics were whole-genome sequenced. The isolates were dominated by species of the P. fluorescens lineage. Isolates susceptible to all antibiotics or resistant to ≥3 antibiotics comprised 20.6% and 24.1%, respectively. The most common resistance was to aztreonam (72.6%), colistin (30.2%), imipenem (25.6%) and meropenem (12.6%). Resistance properties appeared relatively stable over the 26-year study period but with taxa-specific differences. Whole-genome sequencing showed high genome variability, where isolates resistant to ≥3 antibiotics belonged to seven species. A single metallo-betalactmase gene (cphA) was detected, though intrinsic resistance determinants dominated, including resistance–nodulation (RND), ATP-binding cassette (ABC) and small multidrug resistance (Smr) efflux pumps. This study provides further knowledge on the distribution of psychrotrophic Pseudomonas spp. in chicken meat and their antibiotic resistance properties. Further monitoring should be encouraged to determine food as a source of antibiotic resistance and maintain the overall favorable situation with regard to antibiotic resistance in the Norwegian food chain.

Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes

Chicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. Our study represents a proof-of-concept investigation into the possibility and practicality of leveraging microbiome-informed food safety and quality. Through a longitudinal and cross-sectional survey, we established the chicken microbiome as a robust and multifaceted food microbiology attribute that could provide a variety of safety and quality information and retain systematic signals characteristic of overall processing environments.

Microorganisms and their communities on foods are important determinants and indicators of food safety and quality. Despite growing interests in studying food and food-related microbiomes, how effective and practical it is to glean various food safety and quality information from food commodity microbiomes remains underinvestigated. Microbiomes of retail chicken breast from 4 processing establishments in 3 major U.S. broiler production states displayed longitudinal consistency over 7 months and cross-sectional distinctiveness associated with individual processing environments. Packaging type and processing environment but not antibiotic usage and seasonality affected composition and diversity of the microbiomes. Low abundances of antimicrobial resistance genes were found on chicken breasts, and no significant resistome difference was observed between antibiotic-free and conventional products. Benchmarked by culture enrichment, shotgun metagenomics sequencing delivered sensitive and specific detection of Salmonella enterica from chicken breasts.

IMPORTANCE Chicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. Our study represents a proof-of-concept investigation into the possibility and practicality of leveraging microbiome-informed food safety and quality. Through a longitudinal and cross-sectional survey, we established the chicken microbiome as a robust and multifaceted food microbiology attribute that could provide a variety of safety and quality information and retain systematic signals characteristic of overall processing environments.

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 Antimicrobial Resistance in Poultry Farming within Low-Resource Settings

The emergence, spread, and persistence of antimicrobial resistance (AMR) remain a pressing global health issue. Animal husbandry, in particular poultry, makes up a substantial portion of the global antimicrobial use. Despite the growing body of research evaluating the AMR within industrial farming systems, there is a gap in understanding the emergence of bacterial resistance originating from poultry within resource-limited environments. As countries continue to transition from low- to middle income countries (LMICs), there will be an increased demand for quality sources of animal protein. Further promotion of intensive poultry farming could address issues of food security, but it may also increase risks of AMR exposure to poultry, other domestic animals, wildlife, and human populations. Given that intensively raised poultry can function as animal reservoirs for AMR, surveillance is needed to evaluate the impacts on humans, other animals, and the environment. Here, we provide a comprehensive review of poultry production within low-resource settings in order to inform future small-scale poultry farming development. Future research is needed in order to understand the full extent of the epidemiology and ecology of AMR in poultry within low-resource settings.

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.

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.

Aerobic plate count, Salmonella and Campylobacter loads of whole bird carcass rinses from pre-chillers with different water management strategies in a commercial poultry processing plant

Salmonella and Campylobacter are significant issues for poultry processors because of increasing regulatory standards as well as public health concerns. The goal of this study is to report the effects of two different pre-chiller systems that utilize different temperatures and water recirculation systems on whole bird carcass rinsates. Both pre-chiller tanks were contained within a single poultry processing facility and operated at different temperatures and water systems. The incidence of Campylobacter spp. and Salmonella spp., as well as the aerobic plate counts on whole bird carcass rinses are reported in this study from each pre-chiller system. The results from this study reveal that there are significant differences in how microbial populations and pathogens change over time in each pre-chiller system. Furthermore, we identify that these patterns are different per system. Such data are impactful as it indicates that measuring carcasses within a plant must consider both temperature and water recirculation as it may prevent comparability of different lines within a single processing facility.

The Reduction of Pathogen Load on Ross 708 Broilers when Using Different Sources of Commercial Peracetic Acid Sanitizers in a Pilot Processing Plant

Peracetic acid (PAA) in poultry processing is not necessarily the same from company to company. Anecdotal evidence suggests that PeraClean may be more stable compared to the competition; however, it is not known what impact potential differences in chemical stability may have. In order to evaluate the antimicrobial effects of PAA, one PAA (PeraClean, P) was qualitatively compared against two competitor products (Competitors 1 and 2, C1 and C2) at the University of Arkansas Pilot Processing Plant. A total of 150 Ross 708 broilers (42 d) were used in the current study. Briefly, prior to treatment, 10 birds were sampled post-evisceration (C). Then, one of four treatment groups per PAA were applied (A1, A2, B1, and B2). The birds were dipped in either 400 ppm or 600 ppm PAA (A or B), chilled in either 25 ppm or 45 ppm PAA (1 or 2), and then manually agitated in 400 mL of nBPW for 1 min. There were 10 birds per treatment group in total. The resulting rinsates were transported to the Center for Food Safety and assessed for total microbiological load with total aerobic plate counts (Trypticase Soy Agar; APC), coliforms, (Eosin Methylene Blue Media; EMB), Salmonella (Xylose Lysine Deoxycholate agar, XLD), and Campylobacter (modified Charcoal Cefoperazone Deoxycholate Agar, mCCDA). The microbiological plates were incubated as per manufacturer's directions. Statistical analyses were calculated in JMP 14.0, with a significance level of p ≤ 0.05. Data indicate that all three sources of PAA are effective sanitizers for poultry processing applications compared within treatment. Qualitatively, there were differences in efficacy between the treatments. However, additional studies will be required to determine if those differences are quantitatively distinctive and if they are attributable to differences in product stability.

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.