Chapter 10 : Reducing Foodborne Pathogen Persistence and Transmission in Animal Production Environments: Challenges and Opportunities

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Reducing Foodborne Pathogen Persistence and Transmission in Animal Production Environments: Challenges and Opportunities, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555819644/9781555817077_Chap10-1.gif /docserver/preview/fulltext/10.1128/9781555819644/9781555817077_Chap10-2.gif


Preharvest measures to reduce zoonotic pathogens in food animals are critical components in farm-to-table food safety approaches, which recognize that food production and safety occurs along a continuum. The encompassing goal of an integrated food safety program is to improve public health by reducing the risk of human foodborne illness, while the more specific goal of preharvest food safety strategies is to reduce the pathogen load of animals and/or animal products (such as milk or eggs) that are brought to harvest, in order to enhance the efficacy of postharvest interventions and reduce pathogens in the final product. As an example, the presence of pathogens in cattle feces and on cattle hides has been associated with beef carcass contamination ( ). Cattle with high levels of on their hides on entry into commercial processing were often coincident with preevisceration carcasses that were contaminated with the pathogen ( ). Correspondingly, studies conducted in commercial beef processing plants have demonstrated that reducing O157:H7 prevalence on cattle hides reduces its prevalence on resultant carcasses ( ). As another example, the risk of broiler carcass contamination is greater when there is a higher degree of intestinal colonization of birds entering slaughter ( ).

Citation: Berry E, Wells J. 2018. Reducing Foodborne Pathogen Persistence and Transmission in Animal Production Environments: Challenges and Opportunities, p 179-203. In Thakur S, Kniel K (ed), Preharvest Food Safety. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PFS-0006-2014
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1
Figure 1

Persistence and transmission of zoonotic pathogens in food animals and the production environment.

Citation: Berry E, Wells J. 2018. Reducing Foodborne Pathogen Persistence and Transmission in Animal Production Environments: Challenges and Opportunities, p 179-203. In Thakur S, Kniel K (ed), Preharvest Food Safety. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PFS-0006-2014
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Arthur TM,, Bosilevac JM,, Nou X,, Shackelford SD,, Wheeler TL,, Kent MP,, Jaroni D,, Pauling B,, Allen DM,, Koohmaraie M . 2004. Escherichia coli O157 prevalence and enumeration of aerobic bacteria, Enterobacteriaceae, and Escherichia coli O157 at various steps in commercial beef processing plants. J Food Prot 67 : 658 665.[PubMed]
2. Aslam M,, Nattress F,, Greer G,, Yost C,, Gill C,, McMullen L . 2003. Origin of contamination and genetic diversity of Escherichia coli in beef cattle. Appl Environ Microbiol 69 : 2794 2799.[PubMed][CrossRef]
3. Barkocy-Gallagher GA,, Arthur TM,, Siragusa GR,, Keen JE,, Elder RO,, Laegreid WW,, Koohmaraie M . 2001. Genotypic analyses of Escherichia coli O157:H7 and O157 nonmotile isolates recovered from beef cattle and carcasses at processing plants in the Midwestern states of the United States. Appl Environ Microbiol 67 : 3810 3818.[PubMed][CrossRef]
4. Brichta-Harhay DM,, Guerini MN,, Arthur TM,, Bosilevac JM,, Kalchayanand N,, Shackelford SD,, Wheeler TL,, Koohmaraie M . 2008. Salmonella and Escherichia coli O157:H7 contamination on hides and carcasses of cull cattle presented for slaughter in the United States: an evaluation of prevalence and bacterial loads by immunomagnetic separation and direct plating methods. Appl Environ Microbiol 74 : 6289 6297.[PubMed][CrossRef]
5. Nou X,, Rivera-Betancourt M,, Bosilevac JM,, Wheeler TL,, Shackelford SD,, Gwartney BL,, Reagan JO,, Koohmaraie M . 2003. Effect of chemical dehairing on the prevalence of Escherichia coli O157:H7 and the levels of aerobic bacteria and Enterobacteriaceae on carcasses in a commercial beef processing plant. J Food Prot 66 : 2005 2009.[PubMed]
6. Bosilevac JM,, Arthur TM,, Wheeler TL,, Shackelford SD,, Rossman M,, Reagan JO,, Koohmaraie M . 2004. Prevalence of Escherichia coli O157 and levels of aerobic bacteria and Enterobacteriaceae are reduced when hides are washed and treated with cetylpyridinium chloride at a commercial beef processing plant. J Food Prot 67 : 646 650.[PubMed]
7. Bosilevac JM,, Nou X,, Osborn MS,, Allen DM,, Koohmaraie M . 2005. Development and evaluation of an on-line hide decontamination procedure for use in a commercial beef processing plant. J Food Prot 68 : 265 272.[PubMed]
8. Hansson I,, Forshell LP,, Gustafsson P,, Boqvist S,, Lindblad J,, Engvall EO,, Andersson Y,, Vågsholm I . 2007. Summary of the Swedish Campylobacter program in broilers, 2001 through 2005. J Food Prot 70 : 2008 2014.[PubMed]
9. Lindblad M,, Hansson I,, Vågsholm I,, Lindqvist R . 2006. Postchill Campylobacter prevalence on broiler carcasses in relation to slaughter group colonization level and chilling system. J Food Prot 69 : 495 499.[PubMed]
10. Reich F,, Atanassova V,, Haunhorst E,, Klein G . 2008. The effects of Campylobacter numbers in caeca on the contamination of broiler carcasses with Campylobacter. Int J Food Microbiol 127 : 116 120.[PubMed][CrossRef]
11. Anonymous . 1906. Meat Inspection Act of June 30, 1906, 34 Stat. 764, ch. 3913, pp. 674679.
12. Smith DR,, Novotnaj K,, Smith G . 2010. Preharvest food safety: what do the past and the present tell us about the future? J Agromed 15 : 275 280.[PubMed][CrossRef]
13. Oliver SP,, Patel DA,, Callaway TR,, Torrence ME . 2009. ASAS centennial paper: developments and future outlook for preharvest food safety. J Anim Sci 87 : 419 437.[PubMed][CrossRef]
14. U.S. Department of Agriculture, Food Safety and Inspection Service (USDA-FSIS) . 1996. Pathogen reduction; hazard analysis and critical control point (HACCP) systems; final rule. Fed Regist 61 : 3880638989.
15. Koohmaraie M,, Arthur TM,, Bosilevac JM,, Brichta-Harhay DM,, Kalchayanand N,, Shackelford SD,, Wheeler TL . 2007. Interventions to reduce/eliminate Escherichia coli O157:H7 in ground beef. Meat Sci 77 : 90 96.[PubMed][CrossRef]
16. U.S. Department of Agriculture, Food Safety and Inspection Service (USDA-FSIS) . 2012. Shiga toxin-producing Escherichia coli in certain raw beef products. Fed Regist 77 : 3197531981.
17. U.S. Department of Agriculture, Food Safety and Inspection Service (USDA-FSIS) . 2014. Modernization of poultry slaughter inspection; final rule. Fed Regist 79 : 4956649637.
18. Wheeler TL,, Kalchayanand N,, Bosilevac JM . 2014. Pre- and post-harvest interventions to reduce pathogen contamination in the U.S. beef industry. Meat Sci 98 : 372 382.[PubMed][CrossRef]
19. Torrence ME, . 2003. U.S. federal activities, initiatives, and research in food safety, p 3 9. In Torrence ME,, Isaacson RE (ed), Microbial Food Safety in Animal Agriculture: Current Topics. Iowa State Press, Ames, IA.[CrossRef]
20. Binder S,, Khabbaz R,, Swaminathan B,, Tauxe R,, Potter M . 1998. The National Food Safety Initiative. Emerg Infect Dis 4 : 347 349.[PubMed][CrossRef]
21. Institute of Medicine (IOM) and National Research Council (NRC) Committee to Ensure Safety Food from Production to Consumption . 1998. Ensuring safe food from production to consumption. National Academy of Sciences, National Academies Press, Washington, DC.
22. U.S. Department of Agriculture, Food Safety and Inspection Service (USDA-FSIS) . 2015. FSIS Directive 7120.1: safe and suitable ingredients used in the production of meat, poultry, and egg products. http://www.fsis.usda.gov/wps/portal/fsis/topics/regulations/directives/7000-series/safe-suitable-ingredients-related-document.
23. Nutsch AL,, Phebus RK,, Riemann MJ,, Kotrola JS,, Wilson RC,, Boyer JE Jr,, Brown TL . 1998. Steam pasteurization of commercially slaughtered beef carcasses: evaluation of bacterial populations at five anatomical locations. J Food Prot 61 : 571 577.[PubMed]
24. Huffman RD . 2002. Current and future technologies for the decontamination of carcasses and fresh meat. Meat Sci 62 : 285 294.[PubMed][CrossRef]
25. Kalchayanand N,, Arthur TM,, Bosilevac JM,, Schmidt JW,, Wang R,, Shackelford SD,, Wheeler TL . 2012. Evaluation of commonly used antimicrobial interventions for fresh beef inoculated with Shiga toxin-producing Escherichia coli serotypes O26, O45, O103, O111, O121, O145, and O157:H7. J Food Prot 75 : 1207 1212.[PubMed][CrossRef]
26. Pearce RA,, Bolton DJ,, Sheridan JJ,, McDowell DA,, Blair IS,, Harrington D . 2004. Studies to determine the critical control points in pork slaughter hazard analysis and critical control point systems. Int J Food Microbiol 90 : 331 339.[PubMed][CrossRef]
27. Wheatley P,, Giotis ES,, McKevitt AI . 2014. Effects of slaughtering operations on carcass contamination in an Irish pork production plant. Ir Vet J 67 : 1 6.[PubMed][CrossRef]
28. Cox JM,, Pavic A . 2010. Advances in enteropathogen control in poultry production. J Appl Microbiol 108 : 745 755.[PubMed][CrossRef]
29. Hugas M,, Tsigarida E . 2008. Pros and cons of carcass decontamination: the role of the European Food Safety Authority. Meat Sci 78 : 43 52.[PubMed][CrossRef]
30. Sofos JN,, Geornaras I . 2010. Overview of current meat hygiene and safety risks and summary of recent studies on biofilms, and control of Escherichia coli O157:H7 in nonintact, and Listeria monocytogenes in ready-to-eat, meat products. Meat Sci 86 : 2 14.[PubMed][CrossRef]
31. Santini C,, Baffoni L,, Gaggia F,, Granata M,, Gasbarri R,, Di Gioia D,, Biavati B . 2010. Characterization of probiotic strains: an application as feed additives in poultry against Campylobacter jejuni. Int J Food Microbiol 141( Suppl 1) : S98 S108.[PubMed][CrossRef]
32. Zhang G,, Ma L,, Doyle MP . 2007. Salmonellae reduction in poultry by competitive exclusion bacteria Lactobacillus salivarius and Streptococcus cristatus. J Food Prot 70 : 874 878.[PubMed]
33. Casey PG,, Gardiner GE,, Casey G,, Bradshaw B,, Lawlor PG,, Lynch PB,, Leonard FC,, Stanton C,, Ross RP,, Fitzgerald GF,, Hill C . 2007. A five-strain probiotic combination reduces pathogen shedding and alleviates disease signs in pigs challenged with Salmonella enterica serovar Typhimurium. Appl Environ Microbiol 73 : 1858 1863.[PubMed][CrossRef]
34. Scharek-Tedin L,, Pieper R,, Vahjen W,, Tedin K,, Neumann K,, Zentek J . 2013. Bacillus cereus var. Toyoi modulates the immune reaction and reduces the occurrence of diarrhea in piglets challenged with Salmonella Typhimurium DT104. J Anim Sci 91 : 5696 5704.[PubMed][CrossRef]
35. Lema M,, Williams L,, Rao DR . 2001. Reduction of fecal shedding of enterohemorrhagic Escherichia coli O157:H7 in lambs by feeding microbial feed supplement. Small Rumin Res 39 : 31 39.[PubMed][CrossRef]
36. Stephens TP,, Loneragan GH,, Karunasena E,, Brashears MM . 2007. Reduction of Escherichia coli O157 and Salmonella in feces and on hides of feedlot cattle using various doses of a direct-fed microbial. J Food Prot 70 : 2386 2391.[PubMed]
37. Tabe ES,, Oloya J,, Doetkott DK,, Bauer ML,, Gibbs PS,, Khaitsa ML . 2008. Comparative effect of direct-fed microbials on fecal shedding of Escherichia coli O157:H7 and Salmonella in naturally infected feedlot cattle. J Food Prot 71 : 539 544.[PubMed]
38. Pei Y,, Parreira VR,, Roland KL,, Curtiss R III,, Prescott JF . 2014. Assessment of attenuated Salmonella vaccine strains in controlling experimental Salmonella Typhimurium infection in chickens. Can J Vet Res 78 : 23 30.[PubMed]
39. Penha Filho RAC,, de Paiva JB,, da Silva MD,, de Almeida AM,, Berchieri A Jr . 2010. Control of Salmonella Enteritidis and Salmonella Gallinarum in birds by using live vaccine candidate containing attenuated Salmonella Gallinarum mutant strain. Vaccine 28 : 2853 2859.[PubMed][CrossRef]
40. Wyszyńska A,, Raczko A,, Lis M,, Jagusztyn-Krynicka EK . 2004. Oral immunization of chickens with avirulent Salmonella vaccine strain carrying C. jejuni 72Dz/92 cjaA gene elicits specific humoral immune response associated with protection against challenge with wild-type Campylobacter. Vaccine 22 : 1379 1389.[PubMed][CrossRef]
41. Yeh H-Y,, Hiett KL,, Line JE,, Seal BS . 2014. Characterization and reactivity of broiler chicken sera to selected recombinant Campylobacter jejuni chemotactic proteins. Arch Microbiol 196 : 375 383.[PubMed][CrossRef]
42. Husa JA,, Edler RA,, Walter DH,, Holck JT,, Saltzman RJ . 2009. A comparison of the safety, cross-protection, and serologic response associated with two commercial oral Salmonella vaccines in swine. J Swine Health Prod 17 : 10 21.
43. Schwarz P,, Kich JD,, Kolb J,, Cardoso M . 2011. Use of an avirulent live Salmonella Choleraesuis vaccine to reduce the prevalence of Salmonella carrier pigs at slaughter. Vet Rec 169 : 553.[PubMed][CrossRef]
44. Fox JT,, Thomson DU,, Drouillard JS,, Thornton AB,, Burkhardt DT,, Emery DA,, Nagaraja TG . 2009. Efficacy of Escherichia coli O157:H7 siderophore receptor/porin proteins-based vaccine in feedlot cattle naturally shedding E. coli O157. Foodborne Pathog Dis 6 : 893 899.[PubMed][CrossRef]
45. Mizuno T,, McLennan M,, Trott D . 2008. Intramuscular vaccination of young calves with a Salmonella Dublin metabolic-drift mutant provides superior protection to oral delivery. Vet Res 39 : 26.[PubMed][CrossRef]
46. Moxley RA,, Smith DR,, Luebbe M,, Erickson GE,, Klopfenstein TJ,, Rogan D . 2009. Escherichia coli O157:H7 vaccine dose-effect in feedlot cattle. Foodborne Pathog Dis 6 : 879 884.[PubMed][CrossRef]
47. Smith DR,, Moxley RA,, Klopfenstein TJ,, Erickson GE . 2009. A randomized longitudinal trial to test the effect of regional vaccination within a cattle feedyard on Escherichia coli O157:H7 rectal colonization, fecal shedding, and hide contamination. Foodborne Pathog Dis 6 : 885 892.[PubMed][CrossRef]
48. U.S. Department of Agriculture, Food Safety and Inspection Service (USDA-FSIS) . 2014. Pre-harvest management controls and intervention options for reducing Shiga toxin-producing Escherichia coli shedding in cattle: an overview of current research. http://www.fsis.usda.gov/wps/wcm/connect/d5314cc7-1ef7-4586-bca2-f2ed86d9532f/Reducing-Ecoli-Shedding-in-Cattle.pdf?MOD=AJPERES.
49. Thomson DU,, Loneragan GH,, Thornton AB,, Lechtenberg KF,, Emery DA,, Burkhardt DT,, Nagaraja TG . 2009. Use of a siderophore receptor and porin proteins-based vaccine to control the burden of Escherichia coli O157:H7 in feedlot cattle. Foodborne Pathog Dis 6 : 871 877.[PubMed][CrossRef]
50. Vogstad AR,, Moxley RA,, Erickson GE,, Klopfenstein TJ,, Smith DR . 2013. Assessment of heterogeneity of efficacy of a three-dose regimen of a type III secreted protein vaccine for reducing STEC O157 in feces of feedlot cattle. Foodborne Pathog Dis 10 : 678 683.[PubMed][CrossRef]
51. Zuraw L . 2013. Study: E. coli cattle vaccination could prevent 83 percent of human cases. Food Safety News. http://www.foodsafetynews.com/2013/09/e-coli-cattle-vaccination-could-prevent-83-percent-of-human-cases/#.VctuSPnSzJF.
52. U.S. Department of Agriculture, Animal and Plant Health Inspection Service (USDA-APHIS) . 2013. Vaccine usage in U.S. feedlots. http://www.aphis.usda.gov/animal_health/nahms/feedlot/downloads/feedlot2011/Feed11_is_VaccineUsage.pdf.
53. Tonsor GT,, Schroeder TC . 2015. Market impacts of E. coli vaccination in U.S. feedlot cattle. Agric Food Econ 3 : 7.[CrossRef]
54. Callaway TR,, Edrington TS,, Brabban AD,, Anderson RC,, Rossman ML,, Engler MJ,, Carr MA,, Genovese KJ,, Keen JE,, Looper ML,, Kutter EM,, Nisbet DJ . 2008. Bacteriophage isolated from feedlot cattle can reduce Escherichia coli O157:H7 populations in ruminant gastrointestinal tracts. Foodborne Pathog Dis 5 : 183 191.[PubMed][CrossRef]
55. Raya RR,, Oot RA,, Moore-Maley B,, Wieland S,, Callaway TR,, Kutter EM,, Brabban AD . 2011. Naturally resident and exogenously applied T4-like and T5-like bacteriophages can reduce Escherichia coli O157:H7 levels in sheep guts. Bacteriophage 1 : 15 24.[PubMed][CrossRef]
56. Rozema EA,, Stephens TP,, Bach SJ,, Okine EK,, Johnson RP,, Stanford K,, McAllister TA . 2009. Oral and rectal administration of bacteriophages for control of Escherichia coli O157:H7 in feedlot cattle. J Food Prot 72 : 241 250.[PubMed]
57. Albino LAA,, Rostagno MH,, Húngaro HM,, Mendonça RCS . 2014. Isolation, characterization, and application of bacteriophages for Salmonella spp. biocontrol in pigs. Foodborne Pathog Dis 11 : 602 609.[PubMed][CrossRef]
58. Callaway TR,, Edrington TS,, Brabban A,, Kutter B,, Karriker L,, Stahl C,, Wagstrom E,, Anderson R,, Poole TL,, Genovese K,, Krueger N,, Harvey R,, Nisbet DJ . 2011. Evaluation of phage treatment as a strategy to reduce Salmonella populations in growing swine. Foodborne Pathog Dis 8 : 261 266.[PubMed][CrossRef]
59. Atterbury RJ,, Van Bergen MA,, Ortiz F,, Lovell MA,, Harris JA,, De Boer A,, Wagenaar JA,, Allen VM,, Barrow PA . 2007. Bacteriophage therapy to reduce Salmonella colonization of broiler chickens. Appl Environ Microbiol 73 : 4543 4549.[PubMed][CrossRef]
60. Fischer S,, Kittler S,, Klein G,, Glünder G . 2013. Impact of a single phage and a phage cocktail application in broilers on reduction of Campylobacter jejuni and development of resistance. PLoS One 8 : e78543.[PubMed][CrossRef]
61. Loc Carrillo C,, Atterbury RJ,, el-Shibiny A,, Connerton PL,, Dillon E,, Scott A,, Connerton IF . 2005. Bacteriophage therapy to reduce Campylobacter jejuni colonization of broiler chickens. Appl Environ Microbiol 71 : 6554 6563.[PubMed][CrossRef]
62. Callaway TR,, Edrington TS,, Nisbet DJ . 2014. Meat Science and Muscle Biology Symposium: ecological and dietary impactors of foodborne pathogens and methods to reduce fecal shedding in cattle. J Anim Sci 92 : 1356 1365.[PubMed][CrossRef]
63. Anderson RC,, Hume ME,, Genovese KJ,, Callaway TR,, Jung YS,, Edrington TS,, Poole TL,, Harvey RB,, Bischoff KM,, Nisbet DJ . 2004. Effect of drinking-water administration of experimental chlorate ion preparations on Salmonella enterica serovar Typhimurium colonization in weaned and finished pigs. Vet Res Commun 28 : 179 189.[PubMed][CrossRef]
64. Byrd JA,, Burnham MR,, McReynolds JL,, Anderson RC,, Genovese KJ,, Callaway TR,, Kubena LF,, Nisbet DJ . 2008. Evaluation of an experimental chlorate product as a preslaughter feed supplement to reduce salmonella in meat-producing birds. Poult Sci 87 : 1883 1888.[PubMed][CrossRef]
65. Moore RW,, Byrd JA,, Knape KD,, Anderson RC,, Callaway TR,, Edrington T,, Kubena LF,, Nisbet DJ . 2006. The effect of an experimental chlorate product on Salmonella recovery of turkeys when administered prior to feed and water withdrawal. Poult Sci 85 : 2101 2105.[PubMed][CrossRef]
66. Anderson RC,, Callaway TR,, Buckley SA,, Anderson TJ,, Genovese KJ,, Sheffield CL,, Nisbet DJ . 2001. Effect of oral sodium chlorate administration on Escherichia coli O157:H7 in the gut of experimentally infected pigs. Int J Food Microbiol 71 : 125 130.[PubMed][CrossRef]
67. Callaway TR,, Edrington TS,, Anderson RC,, Genovese KJ,, Poole TL,, Elder RO,, Byrd JA,, Bischoff KM,, Nisbet DJ . 2003. Escherichia coli O157:H7 populations in sheep can be reduced by chlorate supplementation. J Food Prot 66 : 194 199.[PubMed]
68. Anderson RC,, Carr MA,, Miller RK,, King DA,, Carstens GE,, Genovese KJ,, Callaway TR,, Edrington TS,, Jung YS,, McReynolds JL,, Hume ME,, Beier RC,, Elder RO,, Nisbet RJ . 2005. Effects of experimental chlorate preparations as feed and water supplements on Escherichia coli colonization and contamination of beef cattle and carcasses. Food Microbiol 22 : 439 447.[CrossRef]
69. Callaway TR,, Anderson RC,, Genovese KJ,, Poole TL,, Anderson TJ,, Byrd JA,, Kubena LF,, Nisbet DJ . 2002. Sodium chlorate supplementation reduces E. coli O157:H7 populations in cattle. J Anim Sci 80 : 1683 1689.[PubMed][CrossRef]
70. Berry ED,, Wells JE . 2010. Escherichia coli O157:H7: recent advances in research on occurrence, transmission, and control in cattle and the production environment. Adv Food Nutr Res 60 : 67 117.[CrossRef]
71. Callaway TR,, Edrington TS,, Anderson RC,, Harvey RB,, Genovese KJ,, Kennedy CN,, Venn DW,, Nisbet DJ . 2008. Probiotics, prebiotics and competitive exclusion for prophylaxis against bacterial disease. Anim Health Res Rev 9 : 217 225.[PubMed][CrossRef]
72. Callaway TR,, Carr MA,, Edrington TS,, Anderson RC,, Nisbet DJ . 2009. Diet, Escherichia coli O157:H7, and cattle: a review after 10 years. Curr Issues Mol Biol 11 : 67 79.[PubMed]
73. Callaway TR,, Anderson RC,, Edrington TS,, Genovese KJ,, Harvey RB,, Poole TL,, Nisbet DJ, . 2013. Novel methods for pathogen control in livestock preharvest: an update, p 275 304. In Sofos J (ed), Advances in Microbial Food Safety, 1st ed. Woodhead Publishing Limited, Sawston, Cambridge, UK.
74. Doyle MP,, Erickson MC . 2006. Reducing the carriage of foodborne pathogens in livestock and poultry. Poult Sci 85 : 960 973.[CrossRef]
75. Doyle MP,, Erickson MC . 2012. Opportunities for mitigating pathogen contamination during on-farm food production. Int J Food Microbiol 152 : 54 74.[PubMed][CrossRef]
76. Jacob ME,, Callaway TR,, Nagaraja TG . 2009. Dietary interactions and interventions affecting Escherichia coli O157 colonization and shedding in cattle. Foodborne Pathog Dis 6 : 785 792.[PubMed][CrossRef]
77. Johnson RP,, Gyles CL,, Huff WE,, Ojha S,, Huff GR,, Rath NC,, Donoghue AM . 2008. Bacteriophages for prophylaxis and therapy in cattle, poultry and pigs. Anim Health Res Rev 9 : 201 215.[PubMed][CrossRef]
78. Larsen MH,, Dalmasso M,, Ingmer H,, Langsrud S,, Malakauskas M,, Mader A,, Møretrø T,, Možina SS,, Rychli K,, Wagner M,, Wallace RJ,, Zentek J,, Jordan K . 2014. Persistence of foodborne pathogens and their control in primary and secondary food production chains. Food Control 44 : 92 109.[CrossRef]
79. World Health Organization, Department of Communicable Disease . 2001. Pre-harvest safety: report of a WHO consultation with the participation of the Food and Agriculture Organization of the United Nations and the Office of International des Epizooties. http://apps.who.int/iris/handle/10665/68889.
80. Beef Industry Food Safety Council (BIFSCO) . 2013. Production best practices (PBP) to aid in the control of foodborne pathogens in groups of cattle. http://www.bifsco.org/CMDocs/BIFSCO/Best%20Practices/Production%20Best%20Practices.pdf.
81. Sparks NHC . 2009. The role of the water supply system in the infection and control of Campylobacter in chicken. Worlds Poult Sci J 65 : 459 473.[CrossRef]
82. Wales AD,, Allen VM,, Davies RH . 2010. Chemical treatment of animal feed and water for the control of Salmonella. Foodborne Pathog Dis 7 : 3 15.[PubMed][CrossRef]
83. Wegener HC,, Hald T,, Lo Fo Wong D,, Madsen M,, Korsgaard H,, Bager F,, Gerner-Smidt P,, Mølbak K . 2003. Salmonella control programs in Denmark. Emerg Infect Dis 9 : 774 780.[PubMed][CrossRef]
84. Hurd HS,, Enøe C,, Sørensen L,, Wachmann H,, Corns SM,, Bryden KM,, Greiner M . 2008. Risk-based analysis of the Danish pork Salmonella program: past and future. Risk Anal 28 : 341 351.[PubMed][CrossRef]
85. Nielsen B,, Alban L,, Stege H,, Sørensen LL,, Møgelmose V,, Bagger J,, Dahl J,, Baggesen DL . 2001. A new Salmonella surveillance and control programme in Danish pig herds and slaughterhouses. Berl Munch Tierarztl Wochenschr 114 : 323 326.[PubMed]
87. Dahl J . 2012. The Danish Salmonella control program: lessons learnt. http://www.pig333.com/salmonella/the-danish-salmonella-control-program-lessons-learnt_5977/.
88. Nielsen TD,, Vesterbæk IL,, Kudahl AB,, Borup KJ,, Nielsen LR . 2012. Effect of management on prevention of Salmonella Dublin exposure of calves during a one-year control programme in 84 Danish dairy herds. Prev Vet Med 105 : 101 109.[PubMed][CrossRef]
89. McGee P,, Scott L,, Sheridan JJ,, Earley B,, Leonard N . 2004. Horizontal transmission of Escherichia coli O157:H7 during cattle housing. J Food Prot 67 : 2651 2656.[PubMed]
90. LeJeune JT,, Wetzel AN . 2007. Preharvest control of Escherichia coli O157 in cattle. J Anim Sci 85( Suppl) : E73 E80.[PubMed][CrossRef]
91. Bach SJ,, Selinger LJ,, Stanford K,, McAllister TA . 2005. Effect of supplementing corn- or barley-based feedlot diets with canola oil on faecal shedding of Escherichia coli O157:H7 by steers. J Appl Microbiol 98 : 464 475.[PubMed][CrossRef]
92. Chase-Topping ME,, McKendrick IJ,, Pearce MC,, MacDonald P,, Matthews L,, Halliday J,, Allison L,, Fenlon D,, Low JC,, Gunn G,, Woolhouse MEJ . 2007. Risk factors for the presence of high-level shedders of Escherichia coli O157 on Scottish farms. J Clin Microbiol 45 : 1594 1603.[PubMed][CrossRef]
93. Chase-Topping M,, Gally D,, Low C,, Matthews L,, Woolhouse M . 2008. Super-shedding and the link between human infection and livestock carriage of Escherichia coli O157. Nat Rev Microbiol 6 : 904 912.[PubMed][CrossRef]
94. Cobbold RN,, Hancock DD,, Rice DH,, Berg J,, Stilborn R,, Hovde CJ,, Besser TE . 2007. Rectoanal junction colonization of feedlot cattle by Escherichia coli O157:H7 and its association with supershedders and excretion dynamics. Appl Environ Microbiol 73 : 1563 1568.[PubMed][CrossRef]
95. Low JC,, McKendrick IJ,, McKechnie C,, Fenlon D,, Naylor SW,, Currie C,, Smith DGE,, Allison L,, Gally DL . 2005. Rectal carriage of enterohemorrhagic Escherichia coli O157 in slaughtered cattle. Appl Environ Microbiol 71 : 93 97.[PubMed][CrossRef]
96. Matthews L,, Low JC,, Gally DL,, Pearce MC,, Mellor DJ,, Heesterbeek JAP,, Chase-Topping M,, Naylor SW,, Shaw DJ,, Reid SW,, Gunn GJ,, Woolhouse ME . 2006. Heterogeneous shedding of Escherichia coli O157 in cattle and its implications for control. Proc Natl Acad Sci USA 103 : 547 552.[PubMed][CrossRef]
97. Stephens TP,, McAllister TA,, Stanford K . 2009. Perineal swabs reveal effect of super shedders on the transmission of Escherichia coli O157:H7 in commercial feedlots. J Anim Sci 87 : 4151 4160.[PubMed][CrossRef]
98. Arthur TM,, Keen JE,, Bosilevac JM,, Brichta-Harhay DM,, Kalchayanand N,, Shackelford SD,, Wheeler TL,, Nou X,, Koohmaraie M . 2009. Longitudinal study of Escherichia coli O157:H7 in a beef cattle feedlot and role of high-level shedders in hide contamination. Appl Environ Microbiol 75 : 6515 6523.[PubMed][CrossRef]
99. Arthur TM,, Brichta-Harhay DM,, Bosilevac JM,, Kalchayanand N,, Shackelford SD,, Wheeler TL,, Koohmaraie M . 2010. Super shedding of Escherichia coli O157:H7 by cattle and the impact on beef carcass contamination. Meat Sci 86 : 32 37.[PubMed][CrossRef]
100. Stephens TP,, McAllister TA,, Stanford K . 2008. Development of an experimental model to assess the ability of Escherichia coli O157:H7-inoculated fecal pats to mimic a super shedder within a feedlot environment. J Food Prot 71 : 648 652.[PubMed]
101. Fox JT,, Renter DG,, Sanderson MW,, Nutsch AL,, Shi X,, Nagaraja TG . 2008. Associations between the presence and magnitude of Escherichia coli O157 in feces at harvest and contamination of preintervention beef carcasses. J Food Prot 71 : 1761 1767.[PubMed]
102. Rice DH,, Sheng HQ,, Wynia SA,, Hovde CJ . 2003. Rectoanal mucosal swab culture is more sensitive than fecal culture and distinguishes Escherichia coli O157:H7-colonized cattle and those transiently shedding the same organism. J Clin Microbiol 41 : 4924 4929.[PubMed][CrossRef]
103. Lim JY,, Li J,, Sheng H,, Besser TE,, Potter K,, Hovde CJ . 2007. Escherichia coli O157:H7 colonization at the rectoanal junction of long-duration culture-positive cattle. Appl Environ Microbiol 73 : 1380 1382.[PubMed][CrossRef]
104. Naylor SW,, Low JC,, Besser TE,, Mahajan A,, Gunn GJ,, Pearce MC,, McKendrick IJ,, Smith DGE,, Gally DL . 2003. Lymphoid follicle-dense mucosa at the terminal rectum is the principal site of colonization of enterohemorrhagic Escherichia coli O157:H7 in the bovine host. Infect Immun 71 : 1505 1512.[PubMed][CrossRef]
105. Davis MA,, Rice DH,, Sheng H,, Hancock DD,, Besser TE,, Cobbold R,, Hovde CJ . 2006. Comparison of cultures from rectoanal-junction mucosal swabs and feces for detection of Escherichia coli O157 in dairy heifers. Appl Environ Microbiol 72 : 3766 3770.[PubMed][CrossRef]
106. Hallewell J,, Niu YD,, Munns K,, McAllister TA,, Johnson RP,, Ackermann H-W,, Thomas JE,, Stanford K . 2014. Differing populations of endemic bacteriophages in cattle shedding high and low numbers of Escherichia coli O157:H7 bacteria in feces. Appl Environ Microbiol 80 : 3819 3825.[PubMed][CrossRef]
107. Arthur TM,, Ahmed R,, Chase-Topping M,, Kalchayanand N,, Schmidt JW,, Bono JL . 2013. Characterization of Escherichia coli O157:H7 strains isolated from supershedding cattle. Appl Environ Microbiol 79 : 4294 4303.[PubMed][CrossRef]
108. Xu Y,, Dugat-Bony E,, Zaheer R,, Selinger L,, Barbieri R,, Munns K,, McAllister TA,, Selinger LB . 2014. Escherichia coli O157:H7 super-shedder and non-shedder feedlot steers harbour distinct fecal bacterial communities. PLoS One 9 : e98115.[PubMed][CrossRef]
109. Pradhan AK,, Mitchell RM,, Kramer AJ,, Zurakowski MJ,, Fyock TL,, Whitlock RH,, Smith JM,, Hovingh E,, Van Kessel JA,, Karns JS,, Schukken YH . 2011. Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis in a longitudinal study of three dairy herds. J Clin Microbiol 49 : 893 901.[PubMed][CrossRef]
110. Mitchell RM,, Whitlock RH,, Stehman SM,, Benedictus A,, Chapagain PP,, Grohn YT,, Schukken YH . 2008. Simulation modeling to evaluate the persistence of Mycobacterium avium subsp. paratuberculosis (MAP) on commercial dairy farms in the United States. Prev Vet Med 83 : 360 380.[PubMed][CrossRef]
111. Lawley TD,, Bouley DM,, Hoy YE,, Gerke C,, Relman DA,, Monack DM . 2008. Host transmission of Salmonella enterica serovar Typhimurium is controlled by virulence factors and indigenous intestinal microbiota. Infect Immun 76 : 403 416.[PubMed][CrossRef]
112. Lawley TD,, Clare S,, Walker AW,, Goulding D,, Stabler RA,, Croucher N,, Mastroeni P,, Scott P,, Raisen C,, Mottram L,, Fairweather NF,, Wren BW,, Parkhill J,, Dougan G . 2009. Antibiotic treatment of Clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts. Infect Immun 77 : 3661 3669.[PubMed][CrossRef]
113. Gautam R,, Kulow M,, Park D,, Gonzales TK,, Dahm J,, Shiroda M,, Stasic AJ,, Döpfer D,, Kaspar CW,, Ivanek R . 2014. Transmission of Escherichia coli O157:H7 in cattle is influenced by the level of environmental contamination. Epidemiol Infect 143 : 274 287.[PubMed][CrossRef]
114. Fecteau M-E,, Whitlock RH,, Buergelt CD,, Sweeney RW . 2010. Exposure of young dairy cattle to Mycobacterium avium subsp. paratuberculosis (MAP) through intensive grazing of contaminated pastures in a herd positive for Johne’s disease. Can Vet J 51 : 198 200.[PubMed]
115. Cobbold RN,, Rice DH,, Davis MA,, Besser TE,, Hancock DD . 2006. Long-term persistence of multi-drug-resistant Salmonella enterica serovar Newport in two dairy herds. J Am Vet Med Assoc 228 : 585 591.[PubMed][CrossRef]
116. Hannah JF,, Wilson JL,, Cox NA,, Richardson LJ,, Cason JA,, Bourassa DV,, Buhr RJ . 2011. Horizontal transmission of Salmonella and Campylobacter among caged and cage-free laying hens. Avian Dis 55 : 580 587.[PubMed][CrossRef]
117. Nayak R,, Stewart-King T . 2008. Molecular epidemiological analysis and microbial source tracking of Salmonella enterica serovars in a preharvest turkey production environment. Foodborne Pathog Dis 5 : 115 126.[PubMed][CrossRef]
118. Nollet N,, Houf K,, Dewulf J,, Duchateau L,, De Zutter L,, De Kruif A,, Maes D . 2005. Distribution of Salmonella strains in farrow-to-finish pig herds: a longitudinal study. J Food Prot 68 : 2012 2021.[PubMed]
119. Berry ED,, Woodbury BL,, Nienaber JA,, Eigenberg RA,, Thurston JA,, Wells JE . 2007. Incidence and persistence of zoonotic bacterial and protozoan pathogens in a beef cattle feedlot runoff control vegetative treatment system. J Environ Qual 36 : 1873 1882.[PubMed][CrossRef]
120. Wang G,, Zhao T,, Doyle MP . 1996. Fate of enterohemorrhagic Escherichia coli O157:H7 in bovine feces. Appl Environ Microbiol 62 : 2567 2570.[PubMed]
121. Kudva IT,, Blanch K,, Hovde CJ . 1998. Analysis of Escherichia coli O157:H7 survival in ovine or bovine manure and manure slurry. Appl Environ Microbiol 64 : 3166 3174.[PubMed]
122. Berry ED,, Miller DN . 2005. Cattle feedlot soil moisture and manure content: II. Impact on Escherichia coli O157. J Environ Qual 34 : 656 663.[PubMed][CrossRef]
123. Ma J,, Mark Ibekwe A,, Crowley DE,, Yang C-H . 2014. Persistence of Escherichia coli O157 and non-O157 strains in agricultural soils. Sci Total Environ 490 : 822 829.[PubMed][CrossRef]
124. Faith NG,, Shere JA,, Brosch R,, Arnold KW,, Ansay SE,, Lee M-S,, Luchansky JB,, Kaspar CW . 1996. Prevalence and clonal nature of Escherichia coli O157:H7 on dairy farms in Wisconsin. Appl Environ Microbiol 62 : 1519 1525.[PubMed]
125. Smith D,, Blackford M,, Younts S,, Moxley R,, Gray J,, Hungerford L,, Milton T,, Klopfenstein T . 2001. Ecological relationships between the prevalence of cattle shedding Escherichia coli O157:H7 and characteristics of the cattle or conditions of the feedlot pen. J Food Prot 64 : 1899 1903.[PubMed]
126. Varel VH,, Wells JE,, Berry ED,, Spiehs MJ,, Miller DN,, Ferrell CL,, Shackelford SD,, Koohmaraie M . 2008. Odorant production and persistence of Escherichia coli in manure slurries from cattle fed zero, twenty, forty, or sixty percent wet distillers grains with solubles. J Anim Sci 86 : 3617 3627.[PubMed][CrossRef]
127. Wells JE,, Shackelford SD,, Berry ED,, Kalchayanand N,, Guerini MN,, Varel VH,, Arthur TM,, Bosilevac JM,, Freetly HC,, Wheeler TL,, Ferrell CL,, Koohmaraie M . 2009. Prevalence and level of Escherichia coli O157:H7 in feces and on hides of feedlot steers fed diets with or without wet distillers grains with solubles. J Food Prot 72 : 1624 1633.[PubMed]
128. Baloda SB,, Christensen L,, Trajcevska S . 2001. Persistence of a Salmonella enterica serovar typhimurium DT12 clone in a piggery and in agricultural soil amended with Salmonella-contaminated slurry. Appl Environ Microbiol 67 : 2859 2862.[PubMed][CrossRef]
129. Inglis GD,, McAllister TA,, Larney FJ,, Topp E . 2010. Prolonged survival of Campylobacter species in bovine manure compost. Appl Environ Microbiol 76 : 1110 1119.[PubMed][CrossRef]
130. Ross CM,, Donnison AM . 2006. Campylobacter jejuni inactivation in New Zealand soils. J Appl Microbiol 101 : 1188 1197.[PubMed][CrossRef]
131. Hutchison ML,, Walters LD,, Moore A,, Crookes KM,, Avery SM . 2004. Effect of length of time before incorporation on survival of pathogenic bacteria present in livestock wastes applied to agricultural soil. Appl Environ Microbiol 70 : 5111 5118.[PubMed][CrossRef]
132. Vivant A-L,, Garmyn D,, Piveteau P . 2013. Listeria monocytogenes, a down-to-earth pathogen. Front Cell Infect Microbiol 3 : 87.[PubMed][CrossRef]
133. Hutchison ML,, Walters LD,, Avery SM,, Synge BA,, Moore A . 2004. Levels of zoonotic agents in British livestock manures. Lett Appl Microbiol 39 : 207 214.[PubMed][CrossRef]
134. Pedersen TB,, Olsen JE,, Bisgaard M . 2008. Persistence of Salmonella Senftenberg in poultry production environments and investigation of its resistance to desiccation. Avian Pathol 37 : 421 427.[PubMed][CrossRef]
135. Dodd CC,, Renter DG,, Shi X,, Alam MJ,, Nagaraja TG,, Sanderson MW . 2011. Prevalence and persistence of Salmonella in cohorts of feedlot cattle. Foodborne Pathog Dis 8 : 781 789.[PubMed][CrossRef]
136. Petersen L,, Wedderkopp A . 2001. Evidence that certain clones of Campylobacter jejuni persist during successive broiler flock rotations. Appl Environ Microbiol 67 : 2739 2745.[PubMed][CrossRef]
137. Hakkinen M,, Hänninen M-L . 2009. Shedding of Campylobacter spp. in Finnish cattle on dairy farms. J Appl Microbiol 107 : 898 905.[PubMed][CrossRef]
138. On SLW,, Atabay HI,, Corry JEL . 1999. Clonality of Campylobacter sputorum bv. paraureolyticus determined by macrorestriction profiling and biotyping, and evidence for long-term persistent infection in cattle. Epidemiol Infect 122 : 175 182.[PubMed][CrossRef]
139. LeJeune JT,, Besser TE,, Rice DH,, Berg JL,, Stilborn RP,, Hancock DD . 2004. Longitudinal study of fecal shedding of Escherichia coli O157:H7 in feedlot cattle: predominance and persistence of specific clonal types despite massive cattle population turnover. Appl Environ Microbiol 70 : 377 384.[PubMed][CrossRef]
140. Carlson BA,, Nightingale KK,, Mason GL,, Ruby JR,, Choat WT,, Loneragan GH,, Smith GC,, Sofos JN,, Belk KE . 2009. Escherichia coli O157:H7 strains that persist in feedlot cattle are genetically related and demonstrate an enhanced ability to adhere to intestinal epithelial cells. Appl Environ Microbiol 75 : 5927 5937.[PubMed][CrossRef]
141. Lahti E,, Ruoho O,, Rantala L,, Hänninen M-L,, Honkanen-Buzalski T . 2003. Longitudinal study of Escherichia coli O157 in a cattle finishing unit. Appl Environ Microbiol 69 : 554 561.[PubMed][CrossRef]
142. Shere JA,, Bartlett KJ,, Kaspar CW . 1998. Longitudinal study of Escherichia coli O157:H7 dissemination on four dairy farms in Wisconsin. Appl Environ Microbiol 64 : 1390 1399.[PubMed]
143. Herbert LJ,, Vali L,, Hoyle DV,, Innocent G,, McKendrick IJ,, Pearce MC,, Mellor D,, Porphyre T,, Locking M,, Allison L,, Hanson M,, Matthews L,, Gunn GJ,, Woolhouse MEJ,, Chase-Topping ME . 2014. E. coli O157 on Scottish cattle farms: evidence of local spread and persistence using repeat cross-sectional data. BMC Vet Res 10 : 95.[PubMed][CrossRef]
144. Wells JE,, Bosilevac JM,, Kalchayanand N,, Arthur TM,, Shackelford SD,, Wheeler TL,, Koohmaraie M . 2009. Prevalence of Mycobacterium avium subsp. paratuberculosis in ileocecal lymph nodes and on hides and carcasses from cull cows and fed cattle at commercial beef processing plants in the United States. J Food Prot 72 : 1457 1462.[PubMed]
145. Smith HW,, Halls S . 1968. The simultaneous oral administration of Salmonella dublin, S. typhimurium and S. choleraesuis to calves and other animals. J Med Microbiol 1 : 203 209.[PubMed][CrossRef]
146. Samuel JL,, O’Boyle DA,, Mathers WJ,, Frost AJ . 1980. Distribution of Salmonella in the carcases of normal cattle at slaughter. Res Vet Sci 28 : 368 372.[PubMed]
147. Arthur TM,, Brichta-Harhay DM,, Bosilevac JM,, Guerini MN,, Kalchayanand N,, Wells JE,, Shackelford SD,, Wheeler TL,, Koohmaraie M . 2008. Prevalence and characterization of Salmonella in bovine lymph nodes potentially destined for use in ground beef. J Food Prot 71 : 1685 1688.[PubMed]
148. Gragg SE,, Loneragan GH,, Brashears MM,, Arthur TM,, Bosilevac JM,, Kalchayanand N,, Wang R,, Schmidt JW,, Brooks JC,, Shackelford SD,, Wheeler TL,, Brown TR,, Edrington TS,, Brichta-Harhay DM . 2013. Cross-sectional study examining Salmonella enterica carriage in subiliac lymph nodes of cull and feedlot cattle at harvest. Foodborne Pathog Dis 10 : 368 374.[PubMed][CrossRef]
149. Bahnson PB,, Fedorka-Cray PJ,, Ladely SR,, Mateus-Pinilla NE . 2006. Herd-level risk factors for Salmonella enterica subsp. enterica in U.S. market pigs. Prev Vet Med 76 : 249 262.[PubMed][CrossRef]
150. Anderson RC,, Genovese KJ,, Harvey RB,, Stanker LH,, DeLoach JR,, Nisbet DJ . 2000. Assessment of the long-term shedding pattern of Salmonella serovar choleraesuis following experimental infection of neonatal piglets. J Vet Diagn Invest 12 : 257 260.[PubMed][CrossRef]
151. Wang B,, Wesley IV,, McKean JD,, O’Connor AM . 2010. Sub-iliac lymph nodes at slaughter lack ability to predict Salmonella enterica prevalence for swine farms. Foodborne Pathog Dis 7 : 795 800.[PubMed][CrossRef]
152. Bahnson PB,, Snyder C,, Omran LM . 2006. Salmonella enterica in superficial cervical (prescapular) and ileocecal lymph nodes of slaughtered pigs. J Food Prot 69 : 925 927.[PubMed]
153. Janss LL,, Bolder NM . 2000. Heritabilities of and genetic relationships between Salmonella resistance traits in broilers. J Anim Sci 78 : 2287 2291.[PubMed][CrossRef]
154. Gast RK,, Holt PS . 1998. Persistence of Salmonella enteritidis from one day of age until maturity in experimentally infected layer chickens. Poult Sci 77 : 1759 1762.[PubMed][CrossRef]
155. Bratz K,, Bücker R,, Gölz G,, Zakrzewski SS,, Janczyk P,, Nöckler K,, Alter T . 2013. Experimental infection of weaned piglets with Campylobacter coli: excretion and translocation in a pig colonisation trial. Vet Microbiol 162 : 136 143.[PubMed][CrossRef]
156. Lin J . 2009. Novel approaches for Campylobacter control in poultry. Foodborne Pathog Dis 6 : 755 765.[PubMed][CrossRef]
157. Freitag NE,, Port GC,, Miner MD . 2009. Listeria monocytogenes: from saprophyte to intracellular pathogen. Nat Rev Microbiol 7 : 623 628.[PubMed][CrossRef]
158. Zundel E,, Bernard S . 2006. Listeria monocytogenes translocates throughout the digestive tract in asymptomatic sheep. J Med Microbiol 55 : 1717 1723.[PubMed][CrossRef]
159. Jeong KC,, Hiki O,, Kang MY,, Park D,, Kaspar CW . 2013. Prevalent and persistent Escherichia coli O157:H7 strains on farms are selected by bovine passage. Vet Microbiol 162 : 912 920.[PubMed][CrossRef]
160. Ravva SV,, Sarreal CZ,, Mandrell RE . 2014. Strain differences in fitness of Escherichia coli O157:H7 to resist protozoan predation and survival in soil. PLoS One 9 : e102412.[CrossRef][PubMed]
161. Lippolis JD,, Brunelle BW,, Reinhardt TA,, Sacco RE,, Nonnecke BJ,, Dogan B,, Simpson K,, Schukken YH . 2014. Proteomic analysis reveals protein expression differences in Escherichia coli strains associated with persistent versus transient mastitis. J Proteomics 108 : 373 381.[PubMed][CrossRef]
162. Fox EM,, Leonard N,, Jordan K . 2011. Physiological and transcriptional characterization of persistent and nonpersistent Listeria monocytogenes isolates. Appl Environ Microbiol 77 : 6559 6569.[PubMed][CrossRef]
163. Tao H,, Bausch C,, Richmond C,, Blattner FR,, Conway T . 1999. Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J Bacteriol 181 : 6425 6440.[PubMed]
164. Hepworth PJ,, Ashelford KE,, Hinds J,, Gould KA,, Witney AA,, Williams NJ,, Leatherbarrow H,, French NP,, Birtles RJ,, Mendonca C,, Dorrell N,, Wren BW,, Wigley P,, Hall N,, Winstanley C . 2011. Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes. Environ Microbiol 13 : 1549 1560.[PubMed][CrossRef]
165. Ihssen J,, Grasselli E,, Bassin C,, François P,, Piffaretti J-C,, Köster W,, Schrenzel J,, Egli T . 2007. Comparative genomic hybridization and physiological characterization of environmental isolates indicate that significant (eco-)physiological properties are highly conserved in the species Escherichia coli. Microbiology 153 : 2052 2066.[PubMed][CrossRef]
166. Bronowski C,, James CE,, Winstanley C . 2014. Role of environmental survival in transmission of Campylobacter jejuni. FEMS Microbiol Lett 356 : 8 19.[PubMed][CrossRef]
167. van Elsas JD,, Semenov AV,, Costa R,, Trevors JT . 2011. Survival of Escherichia coli in the environment: fundamental and public health aspects. ISME J 5 : 173 183.[PubMed][CrossRef]
168. Fan B,, Du Z-Q,, Gorbach DM,, Rothschild MF . 2010. Development and application of high-density SNP arrays in genomic studies of domestic animals. Asian-Aust. J Anim Sci 23 : 833 847.[CrossRef]
169. Jackson BR,, Griffin PM,, Cole D,, Walsh KA,, Chai SJ . 2013. Outbreak-associated Salmonella enterica serotypes and food commodities, United States, 1998–2008. Emerg Infect Dis 19 : 1239 1244.[PubMed][CrossRef]
170. Hafez HM . 1999. Poultry meat and food safety: pre- and post-harvest approaches to reduce foodborne pathogens. Worlds Poult Sci J 55 : 269 280.[CrossRef]
171. Lamont SJ . 1998. Impact of genetics on disease resistance. Poult Sci 77 : 1111 1118.[PubMed][CrossRef]
172. Girard-Santosuosso O,, Lantier F,, Lantier I,, Bumstead N,, Elsen J-M,, Beaumont C . 2002. Heritability of susceptibility to Salmonella enteritidis infection in fowls and test of the role of the chromosome carrying the NRAMP1 gene. Genet Select Evol 34 : 211 219.[CrossRef]
173. Calenge F,, Lecerf F,, Demars J,, Feve K,, Vignoles F,, Pitel F,, Vignal A,, Velge P,, Sellier N,, Beaumont C . 2009. QTL for resistance to Salmonella carrier state confirmed in both experimental and commercial chicken lines. Anim Genet 40 : 590 597.[PubMed][CrossRef]
174. Malek M,, Hasenstein JR,, Lamont SJ . 2004. Analysis of chicken TLR4, CD28, MIF, MD-2, and LITAF genes in a Salmonella enteritidis resource population. Poult Sci 83 : 544 549.[PubMed][CrossRef]
175. Fife MS,, Salmon N,, Hocking PM,, Kaiser P . 2009. Fine mapping of the chicken salmonellosis resistance locus ( SAL1). Anim Genet 40 : 871 877.[PubMed][CrossRef]
176. Swaggerty CL,, Pevzner IY,, He H,, Genovese KJ,, Nisbet DJ,, Kaiser P,, Kogut MH . 2009. Selection of broilers with improved innate immune responsiveness to reduce on-farm infection by foodborne pathogens. Foodborne Pathog Dis 6 : 777 783.[PubMed][CrossRef]
177. Galina-Pantoja L,, Siggens K,, van Schriek MGM,, Heuven HCM . 2009. Mapping markers linked to porcine salmonellosis susceptibility. Anim Genet 40 : 795 803.[PubMed][CrossRef]
178. Uthe JJ,, Wang Y,, Qu L,, Nettleton D,, Tuggle CK,, Bearson SMD . 2009. Correlating blood immune parameters and a CCT7 genetic variant with the shedding of Salmonella enterica serovar Typhimurium in swine. Vet Microbiol 135 : 384 388.[PubMed][CrossRef]
179. Uenishi H,, Shinkai H,, Morozumi T,, Muneta Y . 2012. Genomic survey of polymorphisms in pattern recognition receptors and their possible relationship to infections in pigs. Vet Immunol Immunopathol 148 : 69 73.[PubMed][CrossRef]
180. Flori L,, Gao Y,, Oswald IP,, Lefevre F,, Bouffaud M,, Mercat M-J,, Bidanel J-P,, Rogel-Gaillard C . 2011. Deciphering the genetic control of innate and adaptive immune responses in pig: a combined genetic and genomic study. BMC Proc 5( Suppl 4) : S32.[PubMed][CrossRef]
181. Pighetti GM,, Elliott AA . 2011. Gene polymorphisms: the keys for marker assisted selection and unraveling core regulatory pathways for mastitis resistance. J Mammary Gland Biol Neoplasia 16 : 421 432.[PubMed][CrossRef]
182. Sørensen LP,, Madsen P,, Mark T,, Lund MS . 2009. Genetic parameters for pathogen-specific mastitis resistance in Danish Holstein Cattle. Animal 3 : 647 656.[PubMed][CrossRef]
183. Verbeke J,, Piepers S,, Peelman L,, Van Poucke M,, De Vliegher S . 2012. Pathogen-group specific association between CXCR1 polymorphisms and subclinical mastitis in dairy heifers. J Dairy Res 79 : 341 351.[PubMed][CrossRef]
184. Ley RE,, Lozupone CA,, Hamady M,, Knight R,, Gordon JI . 2008. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6 : 776 788.[PubMed][CrossRef]
185. Rist VTS,, Weiss E,, Eklund M,, Mosenthin R . 2013. Impact of dietary protein on microbiota composition and activity in the gastrointestinal tract of piglets in relation to gut health: a review. Animal 7 : 1067 1078.[PubMed][CrossRef]
186. Bearson SMD,, Allen HK,, Bearson BL,, Looft T,, Brunelle BW,, Kich JD,, Tuggle CK,, Bayles DO,, Alt D,, Levine UY,, Stanton TB . 2013. Profiling the gastrointestinal microbiota in response to Salmonella: low versus high Salmonella shedding in the natural porcine host. Infect Genet Evol 16 : 330 340.[PubMed][CrossRef]
187. Stecher B,, Robbiani R,, Walker AW,, Westendorf AM,, Barthel M,, Kremer M,, Chaffron S,, Macpherson AJ,, Buer J,, Parkhill J,, Dougan G,, von Mering C,, Hardt WD . 2007. Salmonella enterica serovar Typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol 5 : 2177 2189.[PubMed][CrossRef]
188. Endt K,, Stecher B,, Chaffron S,, Slack E,, Tchitchek N,, Benecke A,, Van Maele L,, Sirard JC,, Mueller AJ,, Heikenwalder M,, Macpherson AJ,, Strugnell R,, von Mering C,, Hardt WD . 2010. The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLoS Pathog 6 : e1001097.[CrossRef]
189. May KD,, Wells JE,, Maxwell CV,, Oliver WT . 2012. Granulated lysozyme as an alternative to antibiotics improves growth performance and small intestinal morphology of 10-day-old pigs. J Anim Sci 90 : 1118 1125.[PubMed][CrossRef]
190. Oliver WT,, Wells JE,, Maxwell CV . 2014. Lysozyme as an alternative to antibiotics improves performance in nursery pigs during an indirect immune challenge. J Anim Sci 92 : 4927 4934.[PubMed][CrossRef]
191. Nyachoti CM,, Kiarie E,, Bhandari SK,, Zhang G,, Krause DO . 2012. Weaned pig responses to Escherichia coli K88 oral challenge when receiving a lysozyme supplement. J Anim Sci 90 : 252 260.[PubMed][CrossRef]
192. Maga EA,, Desai PT,, Weimer BC,, Dao N,, Kültz D,, Murray JD . 2012. Consumption of lysozyme-rich milk can alter microbial fecal populations. Appl Environ Microbiol 78 : 6153 6160.[PubMed][CrossRef]
193. Durso LM,, Harhay GP,, Smith TP,, Bono JL,, Desantis TZ,, Harhay DM,, Andersen GL,, Keen JE,, Laegreid WW,, Clawson ML . 2010. Animal-to-animal variation in fecal microbial diversity among beef cattle. Appl Environ Microbiol 76 : 4858 4862.[PubMed][CrossRef]
194. Wells JE,, Shackelford SD,, Berry ED,, Kalchayanand N,, Bosilevac JM,, Wheeler TL . 2011. Impact of reducing the level of wet distillers grains fed to cattle prior to harvest on prevalence and levels of Escherichia coli O157:H7 in feces and on hides. J Food Prot 74 : 1611 1617.[PubMed][CrossRef]
195. Kim M,, Kim J,, Kuehn LA,, Bono JL,, Berry ED,, Kalchayanand N,, Freetly HC,, Benson AK,, Wells JE . 2014. Investigation of bacterial diversity in the feces of cattle fed different diets. J Anim Sci 92 : 683 694.[PubMed][CrossRef]
196. Durso LM,, Wells JE,, Harhay GP,, Rice WC,, Kuehn L,, Bono JL,, Shackelford S,, Wheeler T,, Smith TP . 2012. Comparison of bacterial communities in faeces of beef cattle fed diets containing corn and wet distillers’ grain with solubles. Lett Appl Microbiol 55 : 109 114.[PubMed][CrossRef]
197. Patton TG,, Scupham AJ,, Bearson SM,, Carlson SA . 2009. Characterization of fecal microbiota from a Salmonella endemic cattle herd as determined by oligonucleotide fingerprinting of rDNA genes. Vet Microbiol 136 : 285 292.[PubMed][CrossRef]
198. Stanley D,, Hughes RJ,, Moore RJ . 2014. Microbiota of the chicken gastrointestinal tract: influence on health, productivity and disease. Appl Microbiol Biotechnol 98 : 4301 4310.[PubMed][CrossRef]
199. Danzeisen JL,, Kim HB,, Isaacson RE,, Tu ZJ,, Johnson TJ . 2011. Modulations of the chicken cecal microbiome and metagenome in response to anticoccidial and growth promoter treatment. PLoS One 6 : e27949.[PubMed][CrossRef]
200. Sergeant MJ,, Constantinidou C,, Cogan TA,, Bedford MR,, Penn CW,, Pallen MJ . 2014. Extensive microbial and functional diversity within the chicken cecal microbiome. PLoS One 9 : e91941.[CrossRef][PubMed]
201. Rantala M,, Nurmi E . 1973. Prevention of the growth of Salmonella infantis in chicks by the flora of the alimentary tract of chickens. Br Poult Sci 14 : 627 630.[PubMed][CrossRef]
202. Schneitz C . 2005. Competitive exclusion in poultry: 30 years of research. Food Control 16 : 657 667.[CrossRef]
203. Atterbury RJ,, Hobley L,, Till R,, Lambert C,, Capeness MJ,, Lerner TR,, Fenton AK,, Barrow P,, Sockett RE . 2011. Effects of orally administered Bdellovibrio bacteriovorus on the well-being and Salmonella colonization of young chicks. Appl Environ Microbiol 77 : 5794 5803.[PubMed][CrossRef]
204. Gould LH,, Walsh KA,, Vieira AR,, Herman K,, Williams IT,, Hall AJ,, Cole D, Centers for Disease Control and Prevention . 2013. Surveillance for foodborne disease outbreaks: United States, 1998–2008. MMWR Surveill Summ 62 : 1 34.[PubMed]
205. Painter JA,, Hoekstra RM,, Ayers T,, Tauxe RV,, Braden CR,, Angulo FJ,, Griffin PM . 2013. Attribution of foodborne illnesses, hospitalizations, and deaths to food commodities by using outbreak data, United States, 1998–2008. Emerg Infect Dis 19 : 407 415.[PubMed][CrossRef]
206. O’Connor DR . 2002. A Summary. Report of the Walkerton Inquiry: The Events of May 2000 and Related Issues, Part 1, p 1 35. Ontario Ministry of the Attorney General, Toronto, Ontario.
207. Olson ME,, O’Handley RM,, Ralston BJ,, McAllister TA,, Thompson RCA . 2004. Update on Cryptosporidium and Giardia infections in cattle. Trends Parasitol 20 : 185 191.[PubMed][CrossRef]
208. Jackson SG,, Goodbrand RB,, Johnson RP,, Odorico VG,, Alves D,, Rahn K,, Wilson JB,, Welch MK,, Khakhria R . 1998. Escherichia coli O157:H7 diarrhoea associated with well water and infected cattle on an Ontario farm. Epidemiol Infect 120 : 17 20.[PubMed][CrossRef]
209. Johnson JYM,, Thomas JE,, Graham TA,, Townshend I,, Byrne J,, Selinger LB,, Gannon VPJ . 2003. Prevalence of Escherichia coli O157:H7 and Salmonella spp. in surface waters of southern Alberta and its relation to manure sources. Can J Microbiol 49 : 326 335.[PubMed][CrossRef]
210. Warriner K,, Huber A,, Namvar A,, Fan W,, Dunfield K . 2009. Recent advances in the microbial safety of fresh fruits and vegetables. Adv Food Nutr Res 57 : 155 208.[PubMed][CrossRef]
211. Millner PD,, Karns J, . 2005. Animal manure: bacterial pathogens and disinfection technologies, p 61 83. In Smith JE Jr,, Millner PD,, Jakubowski W,, Goldstein N,, Rynk R (ed), Contemporary Perspectives on Infectious Disease Agents in Sewage Sludge and Manure. Compost Science & Utilization/JG Press, Inc, Emmaus, PA.[PubMed]
212. U.S. Food and Drug Administration (USFDA) . 2015. Food Safety Modernization Act (FSMA) final rule on produce safety. http://www.fda.gov/Food/GuidanceRegulation/FSMA/ucm334114.htm.
213. Jay MT,, Cooley M,, Carychao D,, Wiscomb GW,, Sweitzer RA,, Crawford-Miksza L,, Farrar JA,, Lau DK,, O’Connell J,, Millington A,, Asmundson RV,, Atwill ER,, Mandrell RE . 2007. Escherichia coli O157:H7 in feral swine near spinach fields and cattle, central California coast. Emerg Infect Dis 13 : 1908 1911.[PubMed][CrossRef]