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Olson EG, Dittoe DK, Micciche AC, Stock DA, Rubinelli PM, Rothrock MJ, Ricke SC. Microbiome analyses of poultry feeds: Part II. Comparison of different poultry feeds. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2024; 59:448-482. [PMID: 38840338 DOI: 10.1080/03601234.2024.2361596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/25/2024] [Indexed: 06/07/2024]
Abstract
Within the realm of poultry feed mill operations, the persistent concern over microbial feed quality necessitates the establishment of a robust baseline for enhancing and sustaining the standards of commercial feeds. This dual-phase investigation, comprising Parts I, was previously published, and the current study presented here as Part II aimed to illuminate this baseline using 16S rRNA gene sequencing. In Part II, nine distinct commercial poultry feeds formulated as starters, growers, starter/growers, or supplements, the selected feeds underwent genomic DNA extraction, amplification with custom dual-indexed primers, and subsequent Illumina MiSeq sequencing. Through data analysis in QIIME2-2021.4 and R Studio, the study unveils alpha (Kruskal-Wallis) and beta (ANOSIM) diversity, taxonomic differences (ANCOM), and core microbiomes (core_members), deeming main and pairwise effects statistically significant at p < 0.05 and Q < 0.05. Notably, the investigation identified 30% common core microbial members across the nine feed types, shedding light on potential foodborne poultry pathogens such as Helicobacter and Campylobacter. Probiotic-associated feeds exhibited distinct microbial communities, emphasizing the need to explore their impact on the early poultry gastrointestinal tract (GIT) further.
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Affiliation(s)
- E G Olson
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - D K Dittoe
- Department of Animal Science, Wyoming, University of Wyoming, Laramie, WY, USA
| | - A C Micciche
- Bio-Tech Pharmacal Inc, Fayetteville, Arkansas, USA, Fayetteville, AR, USA
| | - D A Stock
- Department of Biology, Stetson University, DeLand, FL, USA
| | - P M Rubinelli
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR, USA
| | - Michael J Rothrock
- United States Department of Agriculture, Agricultural Research Service, Athens, GA, USA
| | - S C Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
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2
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Vilela FP, Rodrigues DDP, Allard MW, Falcão JP. CRISPR and CRISPR-MVLST reveal conserved spacer distribution and high similarity among Salmonella enterica serovar Infantis genomes from Brazil and other countries. Mol Genet Genomics 2024; 299:61. [PMID: 38806731 DOI: 10.1007/s00438-024-02147-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/24/2024] [Indexed: 05/30/2024]
Abstract
Salmonella enterica serovar Infantis (S. Infantis) is a globally distributed non-typhoid serovar infecting humans and food-producing animals. Considering the zoonotic potential and public health importance of this serovar, strategies to characterizing, monitor and control this pathogen are of great importance. This study aimed to determine the genetic relatedness of 80 Brazilian S. Infantis genomes in comparison to 40 non-Brazilian genomes from 14 countries using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-Multi-Locus Virulence Sequence Typing (CRISPR-MVLST). CRISPR spacers were searched using CRISPR-Cas++ and fimH and sseL alleles using BLAST and MEGA X. Results were analyzed using BioNumerics 7.6 in order to obtain similarity dendrograms. A total of 23 CRISPR1 and 11 CRISPR2 alleles formed by 37 and 26 types of spacers, respectively, were detected. MVLST revealed the presence of five fimH and three sseL alleles. CRISPR's similarity dendrogram showed 32 strain subtypes, with an overall similarity ≥ 78.6. The CRISPR-MVLST similarity dendrogram showed 37 subtypes, with an overall similarity ≥ 79.2. In conclusion, S. Infantis strains isolated from diverse sources in Brazil and other countries presented a high genetic similarity according to CRISPR and CRISPR-MVLST, regardless of their source, year, and/or place of isolation. These results suggest that both methods might be useful for molecular typing S. Infantis strains using WGS data.
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Affiliation(s)
- Felipe Pinheiro Vilela
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, s/n. Bloco S - Sala 41, Ribeirão Preto, SP, 14040-903, Brazil
| | | | - Marc William Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Av. Do Café, s/n. Bloco S - Sala 41, Ribeirão Preto, SP, 14040-903, Brazil.
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3
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Gast RK, Dittoe DK, Ricke SC. Salmonella in eggs and egg-laying chickens: pathways to effective control. Crit Rev Microbiol 2024; 50:39-63. [PMID: 36583653 DOI: 10.1080/1040841x.2022.2156772] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/05/2022] [Indexed: 12/31/2022]
Abstract
Eggs contaminated with Salmonella have been internationally significant sources of human illness for several decades. Most egg-associated illness has been attributed to Salmonella serovar Enteritidis, but a few other serovars (notably S. Heidelberg and S. Typhimurium) are also sometimes implicated. The edible interior contents of eggs typically become contaminated with S. Enteritidis because the pathogen's unique virulence attributes enable it to colonize reproductive tissues in systemically infected laying hens. Other serovars are more commonly associated with surface contamination of eggshells. Both research and field experience have demonstrated that the most effective overall Salmonella control strategy in commercial laying flocks is the application of multiple interventions throughout the egg production cycle. At the preharvest (egg production) level, intervention options of demonstrated efficacy include vaccination and gastrointestinal colonization control via treatments such as prebiotics, probiotics, and bacteriophages, Effective environmental management of housing systems used for commercial laying flocks is also essential for minimizing opportunities for the introduction, transmission, and persistence of Salmonella in laying flocks. At the postharvest (egg processing and handling) level, careful regulation of egg storage temperatures is critical for limiting Salmonella multiplication inside the interior contents.
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Affiliation(s)
- Richard K Gast
- U.S. National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, USA
| | - Dana K Dittoe
- Department of Animal and Dairy Sciences, Meat Science and Animal Biologics Discovery Program, University of Wisconsin, Madison, WI, USA
| | - Steven C Ricke
- Department of Animal and Dairy Sciences, Meat Science and Animal Biologics Discovery Program, University of Wisconsin, Madison, WI, USA
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4
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Pillai N, Ayoola MB, Nanduri B, Rothrock MJ, Ramkumar M. An ensemble learning approach to identify pastured poultry farm practice variables and soil constituents that promote Salmonella prevalence. Heliyon 2022; 8:e11331. [DOI: 10.1016/j.heliyon.2022.e11331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/26/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
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Morita T, Ohyagi N, Matsuura J, Kawaguchi T, Ishizaki N. Salmonella
contamination and hazard analysis in a storage facility for feed materials in Japan. J Appl Microbiol 2022; 133:2966-2978. [DOI: 10.1111/jam.15744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/29/2022] [Accepted: 07/25/2022] [Indexed: 11/27/2022]
Affiliation(s)
- T. Morita
- SETTSU INC., Nishi‐ku, Sakai Osaka Japan
- Faculty of Bioscience and Bioindustry Tokushima University Tokushima Tokushima Japan
| | - N. Ohyagi
- SETTSU INC., Nishi‐ku, Sakai Osaka Japan
| | | | | | - N. Ishizaki
- Faculty of Life and Environmental Science Azabu University Sagamihara Kanagawa Japan
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6
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Coe C, Boltz T, Stearns R, Foster P, Taylor RL, Moritz J, Jaczynski J, Freshour A, Shen C. Thermal inactivation of Salmonella Typhimurium and surrogate Enterococcus faecium in mash broiler feed in a laboratory scale circulated thermal bath. Poult Sci 2022; 101:101976. [PMID: 35759999 PMCID: PMC9249818 DOI: 10.1016/j.psj.2022.101976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 10/26/2022] Open
Abstract
This study compares kinetic parameters of Salmonella and surrogate Enterococcus faecium in mash broiler feed during thermal inactivation. Two-gram samples of mash broiler feed were added into a filtered sample bag and inoculated with nalidixic acid (NaL, 200 ppm) resistant S. Typhimurium or Enterococcus faecium, followed by vacuum-packaging and heating in a circulated thermal water bath at 75°, 85°, and 95°C for 0 to 180 s. Counts of bacterial survival were analyzed on tryptic soy agar and bile esculin agar plus 200 ppm of NaL. Microbial data and thermal kinetic parameters (n = 8, Global-Fit and United States Department of Agriculture [USDA]-Integrated-Predictive-Modeling-Program software) were analyzed by JMP software. Heating mash broiler feed at 75°, 85°, and 95°C decreased (P < 0.05) Salmonella cell counts by >6 log10CFU/g after 180, 60, and 50 s, respectively. Heating E. faecium in feed at 75°, 85°, and 95°C for 180, 120, and 70 s achieved reductions of 3, 6, and >6.5 log10CFU/g, respectively. D-values of linear, Weibull models, and z-value of Salmonella at 75°, 85°, and 95°C were 1.8 to 11.2, 4.2 to 21.8, and 28.6 s, respectively, which were lower (P < 0.05) than those of E. faecium (3.7-18.1, 8.5-34.4, and 34.1 s). Linear with Tail, Linear with Tail and Shoulder, and Weibull with tail equations revealed that E. faecium were more resistant (P < 0.05) to heat than Salmonella as shown by longer "Shoulder-time" (26.5 vs. 16.2 s) and greater "Tail" effect (4.4-4.5 vs. 2.5-2.6 log10CFU/g). Results clearly suggested that E. faecium can be used as a surrogate for Salmonella to validate thermal inactivation during feed manufacture.
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Affiliation(s)
- Corey Coe
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Timothy Boltz
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Rebecca Stearns
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Peighton Foster
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Robert L Taylor
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Joe Moritz
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Jacek Jaczynski
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Annette Freshour
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Cangliang Shen
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
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Shariat NW, Larsen BR, Schaeffer C, Richardson KE. Animal Feed Contains Diverse Populations of
Salmonella. J Appl Microbiol 2022; 132:4476-4485. [DOI: 10.1111/jam.15525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/07/2022] [Accepted: 03/08/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Nikki W. Shariat
- Department of Population Health University of Georgia Athens GA USA
| | - Bryan R. Larsen
- Department of Population Health University of Georgia Athens GA USA
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8
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Olson EG, Dittoe DK, Jendza JA, Stock DA, Ricke SC. Application of Microbial Analyses to Feeds and Potential Implications for Poultry Nutrition. Poult Sci 2022; 101:101789. [PMID: 35346494 PMCID: PMC9079344 DOI: 10.1016/j.psj.2022.101789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Elena G Olson
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Dana K Dittoe
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Joshua A Jendza
- BASF Corporation, 100 Park Avenue, Florham Park, NJ 07932, USA
| | - David A Stock
- Biology Department, Stetson University, Deland, FL 32723, USA
| | - Steven C Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA.
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9
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O'Bryan CA, Ricke SC, Marcy JA. Public health impact of Salmonella spp. on raw poultry: Current concepts and future prospects in the United States. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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10
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Boltz T, Moritz J, Ayres V, Showman C, Jaczynski J, Shen C. Modeling thermal inactivation of Salmonella Typhimurium in mash broiler feed. J APPL POULTRY RES 2021. [DOI: 10.1016/j.japr.2021.100208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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11
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Parker EM, Parker AJ, Short G, O'Connor AM, Wittum TE. Salmonella detection in commercially prepared livestock feed and the raw ingredients and equipment used to manufacture the feed: A systematic review and meta-analysis. Prev Vet Med 2021; 198:105546. [PMID: 34826732 DOI: 10.1016/j.prevetmed.2021.105546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/08/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022]
Abstract
Salmonella contamination of livestock feed is a serious veterinary and public health issue. In this study we used a systematic review to assess the prevalence and characterization of Salmonella isolates detected in raw feed components, feed milling equipment and finished feed from 97 studies published from 1955 to 2020 across seven global regions. Eighty-five studies were included in a meta-analyses to estimate the combined prevalence of Salmonella detection and to compare the risk of contamination associated with different sample types. We found the overall combined prevalence estimate of Salmonella detection was 0.14 with a prevalence of 0.18 in raw feed components, 0.09 in finished feed and 0.08 in feed milling equipment. Animal based raw feed components were 3.9 times more likely to be contaminated with Salmonella than plant based raw feed components. Differences between studies accounted for 99 % of the variance in the prevalence estimate for all sample types and there was no effect of region on the prevalence estimates. The combined prevalence of Salmonella detection in raw feed components decreased from 0.25 in 1955 to 0.11 in 2019. The proportion of Salmonella isolates that were resistant to antimicrobials was largest for amikacin (0.20), tetracycline (0.18) streptomycin (0.17), cefotaxime (0.14) and sulfisoxazole (0.11). The prevalence of Salmonella contamination of animal feed varies widely between individual studies and is an ongoing challenge for the commercial feed industry. Control relies on the vigilant monitoring and control of Salmonella in each individual mill.
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Affiliation(s)
- Elizabeth M Parker
- The Department of Veterinary Preventive Medicine, The Ohio State University, 1920 Coffey Road, Columbus, OH 43210, United States.
| | - Anthony J Parker
- The Department of Animal Science, The Ohio State University, 2029 Fyffe, Columbus, OH 43210, United States
| | - Gwen Short
- The Wooster Campus Research Library, The Ohio State University, 1680 Madison Ave, Wooster, OH 44691, United States
| | - Annette M O'Connor
- Large Animal Clinical Sciences, Michigan State University, 784 Wilson Road, East Lansing, MI 48824, United States
| | - Thomas E Wittum
- The Department of Veterinary Preventive Medicine, The Ohio State University, 1920 Coffey Road, Columbus, OH 43210, United States
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12
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Feye KM, Dittoe DK, Jendza JA, Caldas-Cueva JP, Mallmann BA, Booher B, Tellez-Isaias G, Owens CM, Kidd MT, Ricke SC. A comparison of formic acid or monoglycerides to formaldehyde on production efficiency, nutrient absorption, and meat yield and quality of Cobb 700 broilers. Poult Sci 2021; 100:101476. [PMID: 34710711 PMCID: PMC8560989 DOI: 10.1016/j.psj.2021.101476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/30/2021] [Accepted: 09/03/2021] [Indexed: 11/22/2022] Open
Abstract
After being banned by the European Commission in 2018, the use of formaldehyde as a feed amendment in the United States has come into question. Therefore, this study was conducted to explore alternatives to formaldehyde, such as formic acid and monoglycerides, and their effects on poultry production. In total, 1,728 Cobb 700 broilers were randomly assigned to 96-floor pens on day of hatch (18 birds/pen). Using a randomized complete block design (4 blocks), treatments were assigned to pens with blocking based on location within the barn, with the eastern half of the barn designated for digestibility and the western half designated for production (per experiment: 8 control pens and 10 pens per treatment). All diets were based on a negative control (NC), basal diet. Dietary treatments consisted of: NC, NC + 0.25% formalin (F), NC + 0.25 and 0.50% Amasil NA (AML and AMH; 61% formic acid and 20.5% Na-formate), and NC + SILO Health 104L (SILO; mixture of monoglycerides; 0.5% from 0 to 14 d, 0.4% from 14 to 28 d, and 0.2% from 28 to 42 d). Water and feed were provided ad libitum. Performance data were collected during feed changes on d 0, 14, 28, and 42, with digestibility data collected at d 14 (2 per pen) and carcass quality (6 per pen) assessed at d 46 with a randomly selected group of broilers. A one-way ANOVA followed by Dunnett's multiple comparison, where treatments were evaluated against F were conducted using JMP 14.0 (P ≤ 0.05). Main effect of treatment was significant for performance, nutrient digestibility, and carcass quality. Differences in body weight and ADG were observed from d 14 to d 28, resulting in a trending improvement in lysine digestibility on d 14 and carcass quality on d 46 of birds fed AML and AMH in comparison to those fed F (P < 0.05). Whereas birds fed SILO had reduced digestibility of methionine on d 14 and a decrease in meat quality on d 46 in comparison to those fed F (P < 0.05). Therefore, Amasil NA at 0.25 or 0.50% may be an effective alternative to formaldehyde as a feed amendment for poultry production.
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Affiliation(s)
- K M Feye
- Department of Food Science, University of Arkansas, Fayetteville, AR, USA
| | - D K Dittoe
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - J P Caldas-Cueva
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, USA
| | - B A Mallmann
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, USA
| | - B Booher
- Department of Food Science, University of Arkansas, Fayetteville, AR, USA
| | - G Tellez-Isaias
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, USA
| | - C M Owens
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, USA
| | - M T Kidd
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, USA
| | - S C Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Larsen BR, Richardson KE, Obe T, Schaeffer C, Shariat NW. Mixed
Salmonella
cultures reveal competitive advantages between strains during pre‐enrichment and selective enrichment. J Food Saf 2021. [DOI: 10.1111/jfs.12934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Bryan R. Larsen
- Department of Population Health College of Veterinary Medicine, University of Georgia Athens Georgia USA
| | | | - Tomi Obe
- Department of Population Health College of Veterinary Medicine, University of Georgia Athens Georgia USA
| | | | - Nikki W. Shariat
- Department of Population Health College of Veterinary Medicine, University of Georgia Athens Georgia USA
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