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Microbial Interactions and Management Approaches to Reduce Pathogenic Bacteria in Poultry

Objective 1: Identify/characterize management practices and environmental factors that will reduce fitness characteristics of foodborne pathogens in poultry as related to persistent colonization, survival growth, virulence, and antimicrobial resistance. Sub-objective 1A: Determine the effects of vaccine management programs on the viability of pathogenic bacteria in poultry. Sub-objective 1B: Effect of wood extracts on the viability of pathogenic bacteria in poultry litter. Sub-objective 1C: Identify attractants and spatial distribution of the lesser mealworm. Sub-objective 1D: Determine if Bambermycin in animal feed prevents recipient bacteria from accumulating multiple resistance plasmids, and to determine if multidrug resistant Salmonella lose resistance plasmids when there is no selection pressure. Sub-objective 1E: Determine changes in poultry microbial/fungal digestive populations and identify potential protective isolates against human enteropathogen colonization.

Objective 2: Develop/evaluate new intervention strategies that prevent or reduce enteric colonization and other fitness characteristics that will be integrated into existing management practices and decrease shedding of foodborne pathogens. Sub-objective 2A: Determine the bacteriocidal effects of chitosan as a feed additive against human foodborne enteropathogen colonization in poultry. Sub-objective 2B: Determine the bacteriocidal and anticoccidial effects of chlorate as a feed additive against human foodborne enteropathogen colonization in poultry. Sub-objective 2C: Determine the bacteriocidal effects of clay montomorillonite and calcium formate as feed additives against human foodborne enteropathogen colonization in poultry.

Objective 3: Understand the effect of waste management conditions in poultry (extrinsic and intrinsic) under which foodborne microorganisms exist, and determine the complex interactions among waste management practices on survival and dispersion of pathogens within the poultry facility and the surrounding environment. Sub-objective 3A: Determine the fate and transport into the environment of poultry litter bacteria and the effects of lesser mealworm as a vector. Sub-objective 3B: Modifications of poultry litter composting to increase efficiency and efficacy with respect to reducing pathogen levels.

Objective 4: Determine the complex interactions among fungi/protozoa/microbial population within the gastrointestinal tract of poultry and how it affects food safety. Specifically, research will be focused on understanding the interactions and developing strategies that reduce foodborne pathogens, including antimicrobial resistance. Sub-objective 4A: Identify fungi that will reduce or control the growth of Salmonella and Campylobacter. Sub-objective 4B: Define the role of broiler and layer fungal digestive populations in poultry production and protection against colonization by human foodborne enteropathogens.

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Approach: Objective 1: Management practices and environmental factors and their interactions on the growth of foodborne pathogens in poultry will be evaluated. Broiler chickens will be vaccinated with commercially available vaccines (e.g., Marek's) using several routes of administration and evaluated for Salmonella within the gastrointestinal tract. Beneficial bacteria will be identified from broilers infected with Salmonella and compared to the bacteria found in broilers without Salmonella using a sophisticated DNA technology called pyrosequencing. Pyrosequencing is a method of DNA sequencing (determining the order of nucleotides in DNA) based on the "sequencing by synthesis" principle which will allow the identification of hundreds of bacteria from a single sample. This will lead to the development of new interventions to help control numerous foodborne pathogens. Another approach will investigate the spread of antibiotic resistance from bacteria to bacteria, using an antibiotic (bambermycin) that prevents the transfer of genetic information. Within the environment of broilers, lesser mealworms will be exposed to numerous natural and artificial attractants for the development of new control programs. Poultry are raised on wood flakes that may be contaminated with foodborne pathogens, numerous wood products will be evaluated for their antimicrobial activity against these pathogens using pyrosequencing technology. Objective 2: New intervention strategies will be evaluated to reduce foodborne pathogen colonization in poultry that can be incorporated into existing management practices. Several compounds, including chitosan, chlorate, calcium formate, and clay montomorillonite, will be incorporated into existing commercial management programs. Broilers will be provided the products and challenged with foodborne pathogens and evaluated for the recovery of the pathogens. These compounds utilize different mechanisms for controlling foodborne pathogens, including absorption of the pathogen, targeting enzymatic pathways within the pathogens, and activation of the host immune system. Objective 3: Existing management practices will be evaluated on survival and dispersion of pathogens within the poultry facility and the surrounding environment. Comparisons of management practices on their ability to prevent the spread of pathogenic bacteria and lesser mealworm into the environment will be made using conventional bacterial culture methodology, PCR-based technology, mineral identification, and minimum inhibitory concentration (MIC) analysis. Objective 4: The role of broiler and layer fungal digestive populations in poultry production and protection against colonization by human foodborne enteropathogens will be defined. Using conventional fungal culture methodology, PCR methodology, and sequencing technology fungal species will be identified that have ability to reduce Salmonella and Campylobacter. Building on the information gained in Objective 1, fungal populations recovered in the gastrointestinal tract of broilers taken from Salmonella positive or negative farms will be compared for changes in the fungal profiles using pyrosequencing.
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Byrd, James
Crippen, Tawni
Hume, Michael
Poole, Toni
Sheffield, Cynthia
Project Reports:
Published Journal Articles USDA ARS (NP 108):
Arginine and vitamin E improve the immune response after a Salmonella challenge in broiler chicks
Liu X, Byrd JA, Farnell M, Ruiz-Feria CA.
Poult Sci. 2014 Apr;93(4):882-90.
Delayed insect access alters carrion decomposition and necrophagous insect community assembly
Pechal JL, Benbow ME, Crippen TL, Tarone AM, Tomberlin JK.
Ecosphere. 2014 Apr;5(4):art45.
Full text available in the NAL Digital Collections.
Salmonella Typhimurium in chicken manure reduced or eliminated by addition of LT1000
Sheffield CL, Crippen TL, Beier RC, Byrd JA.
J Appl Poult Res. 2014 Mar;23(1):116-20.
The potential use of bacteria community succession in forensics as described by high throughput metagenomic sequencing
Pechal JL, Crippen TL, Benbow ME, Tarone AM, Dowd S, Tomberlin JK .
Int J Legal Med. 2014 Jan;128(1):193-205.
The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing
Pechal JL, Crippen TL, Benbow ME, Tarone AM, Dowd S, Tomberlin JK.
Int J Legal Med. 2014 Jan;128(1):193-205.
Microbial Community Functional Change during Vertebrate Carrion Decomposition
Pechal JL, Crippen TL, Tarone AM, Lewis AJ, Tomberlin JK, Benbow ME.
PLoS One. 2013 Nov 12;8:e79035.
Effects of broiler feed medications on Salmonella
Volkova VV, Hubbard SA, Magee DL, Byrd Ii JA, Bailey RH, Wills RW .
Avian Dis. 2013 Sep;57(3):640-4.
Microbial volatile emissions as insect semiochemicals
Davis TS, Crippen TL, Hofstetter RW, Tomberlin JK.
J Chem Ecol. 2013 Jul;39(7):840-59.
A survey of bacterial diversity from successive life stages of black soldier fly (Diptera: Stratiomyidae) by using 16S rDNA pyrosequencing
Zheng L, Crippen TL, Singh B, Tarone AM, Dowd S, Yu Z, Wood TK, Tomberlin JK.
J Med Entomol. 2013 May;50(3):647-58.
Quality and safety of broiler meat in various chilling systems
Demirok E, Veluz G, Stuyvenberg WV, Castañeda MP, Byrd A, Alvarado CZ.
Poult Sci. 2013 Apr;92(4):1117-26.
The effect of NovaSil dietary supplementation on the growth and health performance of Nile tilapia (Oreochromis niloticus) fed aflatoxin-B1 contaminated feed
Zychowski KE, Pohlenz C, Maysa T, Romoser A, Hume M, Buentello A, Gatlin III DM, Phillips TD.
Aquaculture. 2013 Feb 15;376:117-23.
Use and misuse of antimicrobial drugs in poultry and livestock: Mechanisms of antimicrobial resistance
Poole T, Sheffield C.
Pak Vet J. 2013;33(3):266-71.
Bacteria mediate oviposition by the black soldier fly, Hermetia illucens (L.), (Diptera: Stratiomyidae)
Zheng L, Crippen TL, Holmes L, Singh B, Pimsler ML, Benbow ME, Tarone AM, Dowd S, Yu Z, Vanlaerhoven SL, Wood TK, Tomberlin JK.
Sci Rep. 2013;3:2563.
Destruction of single-species biofilms of Escherichia coli or Klebsiella pneumoniae subsp. pneumoniae by dextranase, lactoferrin, and lysozyme
Sheffield CL, Crippen TL, Poole TL, Beier RC.
Int Microbiol. 2012 Dec;15(4):185-9.
Interkingdom responses of flies to bacteria mediated by fly physiology and bacterial quorum sensing
Tomberlin JK, Crippen TL, Tarone AM, Singh B, Adams K, Rezenom YH, Benbow ME, Flores M, Longnecker M, Pechal JL, Russell DH, Beier RC, Wood TK.
Anim Behav. 2012 Dec;84(6):1449-56.
Effect of Eimeria infection on cecal microbiome of broilers fed essential oils
Martynova-Van Kley MA, Oviedo-Rondón EO, Dowd SE, Hume M, Nalian A.
Int J Poult Sci. 2012 Dec;11(12):747-55.
Full text available in the NAL Digital Collections.
Survival of O157:H7 and non-O157 serogroups of Escherichia coli in bovine rumen fluid and bile salts
Free AL, Duoss HA, Bergeron LV, Shields-Menard SA, Ward E, Callaway TR, Carroll JA, Schmidt TB, Donaldson JR.
Foodborne Pathog Dis. 2012 Nov;9(11):1010-4.
Effect of supplementation of prebiotic mannan-oligosaccharides and probiotic mixture on growth performance of broilers subjected to chronic heat stress
Sohail MU, Hume ME, Byrd JA, Nisbet DJ, Ijaz A, Sohail A, Shabbir MZ, Rehman H.
Poult Sci. 2012 Sep;91(9):2235-40.
Molecular identification and characterization of ileal and cecal fungus communities in broilers given probiotics, specific essential oil blends, and under mixed Eimeria infection
Hume ME, Hernandez CA, Barbosa NA, Sakomura NK, Dowd SE, Oviedo-Rondón EO.
Foodborne Pathog Dis. 2012 Sep;9(9):853-60.
Proteus mirabilis interkingdom swarming signals attract blow flies
Ma Q, Fonseca A, Liu W, Fields AT, Pimsler ML, Spindola AF, Tarone AM, Crippen TL, Tomberlin JK, Wood TK.
ISME J. 2012 Jul;6(7):1356-66.
Prevalence of Salmonella on retail broiler chicken meat carcasses in Colombia
Donado-Godoy P, Clavijo V, León M, Tafur MA, Gonzales S, Hume M, Alali W, Walls I, Lo Fo Wong DM, Doyle MP.
J Food Prot. 2012 Jun;75(6):1134-8.
Transient gut retention and persistence of Salmonella through metamorphosis in the lesser mealworm, Alphitobius diaperinus (Coleoptera: Tenebrionidae)
Crippen TL, Zheng L, Sheffield CL, Tomberlin JK, Beier RC, Yu Z.
J Appl Microbiol. 2012 May;112(5):920-6.
Single and combined effects of organic selenium and zinc on egg fertility, hatchability, and embryonic mortality of exotic cochin hens
Stanley VG, Hickerson K, Daley MB, Hume M, Hinton A.
Agrotechnology. 2012;2(1):1-3.
The ecology of carrion decomposition
Mondor EB, Tremblay MN, Tomberlin JK, Benbow EM, Tarone AM, Crippen TL.
Nature Education Knowledge. 2012;3(10):21.
Improved visualization of Alphitobius diaperinus (Panzer) (Coleoptera: Tenebrionidae)—part II: alimentary canal components and measurements
Crippen TL, Esquivel JF.
Psyche. 2012;2012:1-8.
Effects of organic selenium and zinc on the aging process of laying hens
Stanley VG, Shanklyn P, Daley M, Gray C, Vaughan V, Hinton Jr A, Hume M.
Agrotechnology. 2012;1(1):1-3.
Effects of dietary supplementation of a commercial prebiotic on survival, growth, immune responses, and gut microbiota of the Pacific white shrimp, Litopenaeus vannamei
Anuta JD, Buentello A, Patnaik S, Hume ME, Mustafa A, Gatlin Iii DM, Lawrence AL .
Aquacult Res. 2011 Dec;42(6):834-44.
Non-Journal Publications:
Invasion and survival of Salmonella in the environment: The role of biofilm - (Book / Chapter)
Sheffield, C.L., Crippen, T.L. 2012. Invasion and survival of Salmonella in the environment: The role of biofilm. In: Kumar, Y., editor. Salmonella-A Diversified Superbug. Rijeka, Croatia: InTech Publishers. p. 3-28.
Lesser mealworms on poultry farms: A potential arena for the dissemination of pathogens and antimicrobial resistance - (Book / Chapter)
Crippen, T.L., Poole, T.L. 2012. Lesser mealworms on poultry farms: A potential arena for the dissemination of pathogens and antimicrobial resistance. In: Callaway, T.R., Edrington, T.S., editors. On-Farm Strategies to Control Foodborne Pathogens. New York, NY: Nova Science Publishers, Inc. p. 233-272.
Food Safety Categories:
Food and Feed Composition and Characteristics
On-Farm Food Safety
Pathogen Biology
Farm-to-Table Categories:
On-farm food production