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Botta C, Buzzanca D, Chiarini E, Chiesa F, Rubiola S, Ferrocino I, Fontanella E, Rantsiou K, Houf K, Alessandria V. Microbial contamination pathways in a poultry abattoir provided clues on the distribution and persistence of Arcobacter spp. Appl Environ Microbiol 2024; 90:e0029624. [PMID: 38647295 PMCID: PMC11107157 DOI: 10.1128/aem.00296-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
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.
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Affiliation(s)
- Cristian Botta
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Davide Buzzanca
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Elisabetta Chiarini
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Francesco Chiesa
- Department of Veterinary Sciences, University of Torino, Torino, Italy
| | - Selene Rubiola
- Department of Veterinary Sciences, University of Torino, Torino, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | | | - Kalliopi Rantsiou
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Kurt Houf
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Valentina Alessandria
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
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Jeong J, Song H, Kim WH, Chae M, Lee JY, Kwon YK, Cho S. Tracking the contamination sources of microbial population and characterizing Listeria monocytogenes in a chicken slaughterhouse by using culture-dependent and -independent methods. Front Microbiol 2023; 14:1282961. [PMID: 38098672 PMCID: PMC10720907 DOI: 10.3389/fmicb.2023.1282961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023] Open
Abstract
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.
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Affiliation(s)
- Jiyeon Jeong
- Avian Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Hyokeun Song
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Woo-Hyun Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Myeongju Chae
- Avian Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
| | - Ji-Youn Lee
- Avian Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
| | - Yong-Kuk Kwon
- Avian Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
| | - Seongbeom Cho
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
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3
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Xu X, Rothrock MJ, Mishra A, Kumar GD, Mishra A. Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessment. J Food Prot 2023; 86:100169. [PMID: 37774838 DOI: 10.1016/j.jfp.2023.100169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023]
Abstract
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.
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Affiliation(s)
- Xinran Xu
- Department of Food Science and Technology, University of Georgia, Athens, GA, USA
| | - Michael J Rothrock
- Egg Safety and Quality Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, USA
| | - Aditya Mishra
- Department of Statistics, University of Georgia, Athens, GA, USA
| | | | - Abhinav Mishra
- Department of Food Science and Technology, University of Georgia, Athens, GA, USA.
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Gichure JN, Coorey R, Njage PMK, Dykes GA, Muema EK, Buys EM. The Microbial Genetic Diversity and Succession Associated with Processing Waters at Different Broiler Processing Stages in an Abattoir in Australia. Pathogens 2023; 12:pathogens12030488. [PMID: 36986410 PMCID: PMC10053010 DOI: 10.3390/pathogens12030488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
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.
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Affiliation(s)
- Josphat Njenga Gichure
- Department of Consumer and Food Sciences, University of Pretoria, Hatfield 0028, South Africa
- Department of Food Science, Nutrition and Technology, South Eastern Kenya University, Kitui P.O. Box 170-90200, Kenya
| | - Ranil Coorey
- School of Molecular and Life Sciences, Faculty of Science and Engineering, Curtin University, Perth 6845, Australia
| | - Patrick Murigu Kamau Njage
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gary A Dykes
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia 4067, Australia
| | - Esther K Muema
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield 0028, South Africa
| | - Elna M Buys
- Department of Consumer and Food Sciences, University of Pretoria, Hatfield 0028, South Africa
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5
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Cano C, Sadat R, Chaves BD. Peroxyacetic Acid Effectiveness against Salmonella on Raw Poultry Parts Is Not Affected by Organic Matter. J Food Prot 2022; 85:1446-1451. [PMID: 35880909 DOI: 10.4315/jfp-22-123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/18/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Organic matter (OM) accumulation is common in chill tanks used to decontaminate raw poultry parts during processing. OM negatively affects the antimicrobial activity of chlorine-based compounds, but its effect on the antimicrobial effectiveness of peroxyacetic acid (PAA) on poultry meat has not been described. Therefore, this study evaluated the effect of OM on the efficacy of PAA solutions in simulated postchill tanks to reduce Salmonella artificially inoculated onto chicken parts. Chicken thighs were inoculated with a five-strain cocktail of poultry-borne Salmonella enterica serovars at ca. 6 log CFU/mL. Then, the thighs were immersed for 30 or 45 s in PAA solutions (500 or 1,000 ppm) with chicken slurry to simulate OM accumulation (0, 15, or 30 g/L). The thighs were rinsed with neutralizing buffered peptone water (100 mL), and rinsates were plated onto xylose lysine desoxycholate agar. Experiments were performed in triplicate (three thighs per treatment per replicate). Chemical oxygen demand, total nitrogen, and pH were measured as the water quality parameters of the PAA solutions before and after use. Chemical oxygen demand ranged from 2,905 mg/L in unused 500-ppm solutions without added OM to 6,290 mg/L in used 1,000-ppm solutions with 30 g/L OM. Initial total nitrogen was 42.5 ± 2.0 and 60.9 ± 8.3 mg/L for 15 and 30 g/L OM, which increased by 27 ± 17 mg/L after use. The pH of solutions ranged from 3.16 ± 0.14 to 3.42 ± 0.09 for the 1,000-ppm solutions and from 3.59 ± 0.06 to 3.96 ± 0.06 for the 500-ppm solutions. Mean Salmonella reductions were 0.9 ± 0.1 log CFU/mL of rinsate for the 500-ppm PAA treatment and 1.1 ± 0.1 log CFU/mL of rinsate for 1,000-ppm PAA treatment. Exposure time did not have a significant effect on the logarithmic reductions. There was no significant effect of OM concentration (P > 0.05) on the reductions, indicating that the antimicrobial efficacy was not affected and that PAA solutions may continue to be reused as long as the PAA concentration is actively monitored. HIGHLIGHTS
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Affiliation(s)
- Carmen Cano
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Raziya Sadat
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Byron D Chaves
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
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6
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Bacterial community identification in poultry carcasses using high-throughput next generation sequencing. Int J Food Microbiol 2022; 364:109533. [DOI: 10.1016/j.ijfoodmicro.2022.109533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 11/24/2022]
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7
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Practical Opportunities for Microbiome Analyses and Bioinformatics in Poultry Processing. Poult Sci 2022; 101:101787. [PMID: 35346493 PMCID: PMC9079351 DOI: 10.1016/j.psj.2022.101787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 11/21/2022] Open
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8
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Weinroth MD, Belk AD, Dean C, Noyes N, Dittoe DK, Rothrock MJ, Ricke SC, Myer PR, Henniger MT, Ramírez GA, Oakley BB, Summers KL, Miles AM, Ault-Seay TB, Yu Z, Metcalf JL, Wells JE. Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies. J Anim Sci 2022; 100:skab346. [PMID: 35106579 PMCID: PMC8807179 DOI: 10.1093/jas/skab346] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/19/2021] [Indexed: 12/13/2022] Open
Abstract
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.
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Affiliation(s)
- Margaret D Weinroth
- U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center (USNPRC), Athens, GA 30605, USA
| | - Aeriel D Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80524, USA
- Joint Institute of Food Safety and Applied Nutrition, University of Maryland, College Park, MD 20740, USA
| | - Chris Dean
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Noelle Noyes
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Dana K Dittoe
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Michael J Rothrock
- U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center (USNPRC), Athens, GA 30605, USA
| | - Steven C Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Phillip R Myer
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
| | - Madison T Henniger
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
| | - Gustavo A Ramírez
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Brian B Oakley
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Katie Lynn Summers
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center (BARC), Beltsville, MD 20705, USA
| | - Asha M Miles
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center (BARC), Beltsville, MD 20705, USA
| | - Taylor B Ault-Seay
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80524, USA
| | - James E Wells
- USDA ARS US Meat Animal Research Center (USMARC), Clay Center, NE 68933, USA
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Gichure JN, Kamau Njage PM, Wambui JM, Dykes GA, Buys EM, Coorey R. Systematic-review and meta-analysis on effect of decontamination interventions on prevalence and concentration of Campylobacter spp. during primary processing of broiler chickens. Food Microbiol 2021; 102:103923. [PMID: 34809949 DOI: 10.1016/j.fm.2021.103923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022]
Abstract
Scientific advances in pathogen decontamination offer great potential to reduce Campylobacter spp. during primary processing. The aim of this study was to collate data from eligible studies using systematic review, meta-analysis followed by meta-regression. Random effect meta-analysis revealed heterogenous (τ2 = 0.6, I2 = 98 %) pooled reduction in Campylobacter concentration of 0.6 log10 CFU/carcass and a decrease in relative risk of Campylobacter spp. prevalence in broiler carcasses by 57.2 %. Decontamination interventions during Inside-Outside-Carcass-Wash were most effective on concentration (0.8 log10 CFU/carcass) while those during evisceration were most effective on prevalence (78.0 % decrease in relative risk). Physical decontamination was more effective on Campylobacter prevalence (68.7 % decrease in relative risk) compared chemical treatment (30.3 %). Application through immersion was superior on Campylobacter concentration (0.9 log10 CFU/carcass odds reduction) to spraying (0.5 log10 CFU/carcass odds reduction). Publication bias and small study effect were observed in trials on Campylobacter prevalence but not for concentration. The meta-regression revealed four and seven potential modifier variables for concentration and prevalence respectively. This meta-analysis provides an overview of the expected magnitude in Campylobacter spp. concentration and prevalence with application of decontamination interventions on broiler carcasses along the slaughter process and forms a basis of quantitative microbial risk assessment and derivation of intervention measures. Even though modest microbial concentration reduction is reported there was a large decrease in contamination prevalence during processing interventions.
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Affiliation(s)
- Josphat N Gichure
- Department of Food Science, Nutrition and Technology, South Eastern Kenya University, P.O. Box 170-90200, Kitui, Kenya.
| | - Patrick Murigu Kamau Njage
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, Denmark
| | - Joseph M Wambui
- Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, 8057, Zurich, Switzerland
| | - Gary A Dykes
- School of Molecular and Life Sciences, Faculty of Science and Engineering, Curtin University, GPO Box U1987, Perth, Western Australia, 6845, Australia
| | - Elna M Buys
- Department of Consumer and Food Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Ranil Coorey
- School of Molecular and Life Sciences, Faculty of Science and Engineering, Curtin University, GPO Box U1987, Perth, Western Australia, 6845, Australia
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Wythe LA, Dittoe DK, Feye KM, Olson EG, Perry LM, Ricke SC. Reduction of Salmonella Infantis on skin-on, bone-in chicken thighs by cetylpyridinium chloride application and the impact on the skin microbiota. Poult Sci 2021; 101:101409. [PMID: 34953376 PMCID: PMC8715379 DOI: 10.1016/j.psj.2021.101409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 01/04/2023] Open
Abstract
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.
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Affiliation(s)
- L A Wythe
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706
| | - D K Dittoe
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706
| | - K M Feye
- Department of Food Science and Center for Food Safety, University of Arkansas, Fayetteville, AR 72704
| | - E G Olson
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706
| | - L M Perry
- Safe Foods Corporation, Little Rock, AR 72114
| | - S C Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706.
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11
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Song X, Wang H, Xu X. Investigation of microbial contamination in a chicken slaughterhouse environment. J Food Sci 2021; 86:3598-3610. [PMID: 34287883 DOI: 10.1111/1750-3841.15842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/04/2021] [Accepted: 06/13/2021] [Indexed: 12/01/2022]
Abstract
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.
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Affiliation(s)
- Xiangyu Song
- Key Laboratory of Animal Products Processing, Ministry of Agriculture, Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Jiangsu Synergetic Innovation Center of Meat Production and Processing, and College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China
| | - Huhu Wang
- Key Laboratory of Animal Products Processing, Ministry of Agriculture, Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Jiangsu Synergetic Innovation Center of Meat Production and Processing, and College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China
| | - Xinglian Xu
- Key Laboratory of Animal Products Processing, Ministry of Agriculture, Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Jiangsu Synergetic Innovation Center of Meat Production and Processing, and College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China
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12
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The changing microbiome of poultry meat; from farm to fridge. Food Microbiol 2021; 99:103823. [PMID: 34119108 DOI: 10.1016/j.fm.2021.103823] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 11/20/2022]
Abstract
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.
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Chen SH, Fegan N, Kocharunchitt C, Bowman JP, Duffy LL. Impact of Poultry Processing Operating Parameters on Bacterial Transmission and Persistence on Chicken Carcasses and Their Shelf Life. Appl Environ Microbiol 2020; 86:e00594-20. [PMID: 32276979 PMCID: PMC7267199 DOI: 10.1128/aem.00594-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/03/2020] [Indexed: 01/23/2023] Open
Abstract
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.
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Affiliation(s)
- Stanley H Chen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Coopers Plains, Queensland, Australia
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Narelle Fegan
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Coopers Plains, Queensland, Australia
| | - Chawalit Kocharunchitt
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - John P Bowman
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Lesley L Duffy
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Coopers Plains, Queensland, Australia
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Changes in the microbial communities of air- and water-chilled yellow-feathered broilers during storage at 2 °C. Food Microbiol 2020; 87:103390. [DOI: 10.1016/j.fm.2019.103390] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/20/2019] [Accepted: 11/20/2019] [Indexed: 01/06/2023]
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15
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Chen SH, Fegan N, Kocharunchitt C, Bowman JP, Duffy LL. Changes of the bacterial community diversity on chicken carcasses through an Australian poultry processing line. Food Microbiol 2020; 86:103350. [DOI: 10.1016/j.fm.2019.103350] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 10/03/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023]
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Feye KM, Thompson DR, Rothrock MJ, Kogut MH, Ricke SC. Poultry processing and the application of microbiome mapping. Poult Sci 2020; 99:678-688. [PMID: 32029154 PMCID: PMC7587767 DOI: 10.1016/j.psj.2019.12.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Indexed: 01/28/2023] Open
Abstract
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.
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Affiliation(s)
- K M Feye
- Southern Plains Agricultural Research Center, USDA-ARS, Athens, TX 30605
| | - D R Thompson
- Department of Computer Science and Engineering, University of Arkansas, Fayetteville, AR 72704
| | - M J Rothrock
- US National Poultry Research Center, Egg Safety and Quality Research, USDA-ARS, Athens, GA 30605
| | - M H Kogut
- Southern Plains Agricultural Research Center, USDA-ARS, Athens, TX 30605
| | - S C Ricke
- Center for Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR 72704.
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Wang H, Qin X, Mi S, Li X, Wang X, Yan W, Zhang C. Contamination of yellow-feathered broiler carcasses: Microbial diversity and succession during processing. Food Microbiol 2019; 83:18-26. [DOI: 10.1016/j.fm.2019.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 12/22/2022]
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Rothrock MJ, Locatelli A, Feye KM, Caudill AJ, Guard J, Hiett K, Ricke SC. A Microbiomic Analysis of a Pasture-Raised Broiler Flock Elucidates Foodborne Pathogen Ecology Along the Farm-To-Fork Continuum. Front Vet Sci 2019; 6:260. [PMID: 31448296 PMCID: PMC6692657 DOI: 10.3389/fvets.2019.00260] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 07/24/2019] [Indexed: 01/09/2023] Open
Abstract
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.
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Affiliation(s)
- Michael J. Rothrock
- Egg Safety and Quality Research Unit, U. S. National Poultry Research Center, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Athens, GA, United States
| | - Aude Locatelli
- Egg Safety and Quality Research Unit, U. S. National Poultry Research Center, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Athens, GA, United States
| | - Kristina M. Feye
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, United States
| | - Andrew J. Caudill
- Department of Public Health, University of Georgia, Athens, GA, United States
| | - Jean Guard
- Egg Safety and Quality Research Unit, U. S. National Poultry Research Center, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Athens, GA, United States
| | - Kelli Hiett
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration (FDA), Laurel, MD, United States
| | - Steven C. Ricke
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, United States
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Rothrock MJ, Micciche AC, Bodie AR, Ricke SC. Listeria Occurrence and Potential Control Strategies in Alternative and Conventional Poultry Processing and Retail. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00033] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Handley JA, Park SH, Kim SA, Ricke SC. Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms. Front Microbiol 2018; 9:345. [PMID: 29552001 PMCID: PMC5841210 DOI: 10.3389/fmicb.2018.00345] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/12/2018] [Indexed: 12/14/2022] Open
Abstract
Commercial poultry abattoirs were evaluated to determine the efficacy of the multi-hurdle antimicrobial strategy employed to reduce the microbial load present on incoming broilers from the farm. As next generation sequencing (NGS) has been recently employed to characterize the poultry production system, this study utilized 16S High throughput sequencing (HTS) and quantitative plating data to profile the microbiota of chicken carcasses and determine the efficacy of the multi-hurdle antimicrobial system. Aerobic plate count (APC) and Enterobacteriaceae (EB) microbial counts were quantified from whole bird carcass rinsates (WBCR). The remaining rinsates underwent microbiome analysis using 16S rRNA gene fragments on an Illumina MiSeq and were analyzed by Quantitative Insights into Microbial Ecology (QIIME). The key stages of processing were determined to be at rehang, pre-chill, and post-chill as per the Salmonella Reduction Regulation (75 Fed. Reg. 27288-27294). The APC microbial data from rehang, pre-chill, and post-chill were mean log 4.63 CFU/mL, 3.21 CFU/mL, and 0.89 CFU/mL and EB counts were mean log 2.99 CFU/mL, 1.95 CFU/mL, and 0.35 CFU/mL. NGS of WBCR identified 222 Operational Taxonomic Units' (OTU's) of which only 23 OTU's or 10% of the population was recovered post-chill. Microbiome data suggested a high relative abundance of Pseudomonas at post-chill. Additionally, Pseudomonas, Enterobacteriaceae, and Weeksellaceae Chryseobacterium have been identified as potential indicator organisms having been isolated from all processing abattoirs and sampling locations. This study provides insight into the microbiota of commercial broilers during poultry processing.
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Affiliation(s)
| | | | | | - Steven C. Ricke
- Center for Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR, United States
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Possas A, Carrasco E, García-Gimeno R, Valero A. Models of microbial cross-contamination dynamics. Curr Opin Food Sci 2017. [DOI: 10.1016/j.cofs.2017.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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22
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Ae Kim S, Hong Park S, In Lee S, Owens CM, Ricke SC. Assessment of Chicken Carcass Microbiome Responses During Processing in the Presence of Commercial Antimicrobials Using a Next Generation Sequencing Approach. Sci Rep 2017; 7:43354. [PMID: 28230180 PMCID: PMC5322484 DOI: 10.1038/srep43354] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/23/2017] [Indexed: 12/26/2022] Open
Abstract
The purpose of this study was to 1) identify microbial compositional changes on chicken carcasses during processing, 2) determine the antimicrobial efficacy of peracetic acid (PAA) and Amplon (blend of sulfuric acid and sodium sulfate) at a poultry processing pilot plant scale, and 3) compare microbial communities between chicken carcass rinsates and recovered bacteria from media. Birds were collected from each processing step and rinsates were applied to estimate aerobic plate count (APC) and Campylobacter as well as Salmonella prevalence. Microbiome sequencing was utilized to identify microbial population changes over processing and antimicrobial treatments. Only the PAA treatment exhibited significant reduction of APC at the post chilling step while both Amplon and PAA yielded detectable Campylobacter reductions at all steps. Based on microbiome sequencing, Firmicutes were the predominant bacterial group at the phyla level with over 50% frequency in all steps while the relative abundance of Proteobacteria decreased as processing progressed. Overall microbiota between rinsate and APC plate microbial populations revealed generally similar patterns at the phyla level but they were different at the genus level. Both antimicrobials appeared to be effective on reducing problematic bacteria and microbiome can be utilized to identify optimal indicator microorganisms for enhancing product quality.
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Affiliation(s)
- Sun Ae Kim
- Center for Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR 72704 USA
| | - Si Hong Park
- Center for Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR 72704 USA
| | - Sang In Lee
- Center for Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR 72704 USA
| | - Casey M. Owens
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701 USA
| | - Steven C. Ricke
- Center for Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR 72704 USA
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