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

References

• Abdelsattar, A. S., F. Abdelrahman, A. Dawoud, I. F. Connerton, and A. El-Shibiny. 2019. Encapsulation of E. coli phage ZCEC5 in chitosan-alginate beads as a delivery system in phage therapy. AMB Express 9 (1):87. doi: 10.1186/s13568-019-0810-9.
   PubMedGoogle Scholar
• Ackermann, H. W. 2009. Phage classification and characterization. Methods in Molecular Biology (Clifton, N.J.) 501:127–40. doi: 10.1007/978-1-60327-164-6_13.
   PubMedGoogle Scholar
• Ackermann, H. W., and D. Prangishvili. 2012. Prokaryote viruses studied by electron microscopy. Archives of Virology 157 (10):1843–9. doi: 10.1007/s00705-012-1383-y.
   PubMed Web of Science ®Google Scholar
• Ackermann, H. W., D. Tremblay, and S. Moineau. 2004. Long-term bacteriophage preservation. WFCC Newsletter 38:35–40.
   Google Scholar
• Agyare, C., V. E. Boamah, C. N. Zumbi, and F. Boateng Osei. 2018. Antibiotic use in poultry production and its effects on bacterial resistance. In Antimicrobial resistance—A global threat, ed. Y. Kumar. London, UK: IntechOpen. doi: 10.5772/intechopen.79371.https://www.intechopen.com/books/antimicrobial-resistance-a-global-threat/antibiotic-use-in-poultry-production-and-its-effects-on-bacterial-resistance.
   Google Scholar
• Ahmadi, M., M. A. Karimi Torshizi, S. Rahimi, and J. J. Dennehy. 2016. Prophylactic bacteriophage administration more effective than post-infection administration in reducing Salmonella enterica serovar Enteritidis shedding in quail. Frontiers in Microbiology 7:1253. doi: 10.3389/fmicb.2016.01253.
   PubMed Web of Science ®Google Scholar
• Ajuebor, J., O. McAuliffe, J. O’Mahony, R. P. Ross, C. Hill, and A. Coffey. 2016. Bacteriophage endolysins and their applications. Science Progress 99 (2):183–99. doi: 10.3184/003685016X14627913637705.
   PubMed Web of Science ®Google Scholar
• Al-Khalaifah, H. S. 2018. Benefits of probiotics and/or prebiotics for antibiotic-reduced poultry. Poultry Science 97 (11):3807–15. doi: 10.3382/ps/pey160.
   PubMed Web of Science ®Google Scholar
• Alexandratos, N., and J. Brunisma. 2012. World agriculture towards 2030/2050: The 2012 revision. Retrieved from Food and Agriculture Organization of the United Nations. ESA working paper no. 12-03:2012. www.fao.org/economic/esa.
   Google Scholar
• Andreatti Filho, R. L., J. P. Higgins, S. E. Higgins, G. Gaona, A. D. Wolfenden, G. Tellez, and B. M. Hargis. 2007. Ability of bacteriophages isolated from different sources to reduce Salmonella enterica serovar enteritidis in vitro and in vivo. Poultry Science 86 (9):1904–9. doi: 10.1093/ps/86.9.1904.
   PubMed Web of Science ®Google Scholar
• Aslam, B., W. Wang, M. I. Arshad, M. Khurshid, S. Muzammil, M. H. Rasool, M. A. Nisar, R. F. Alvi, M. A. Aslam, M. U. Qamar, et al. 2018. Antibiotic resistance: A rundown of a global crisis. Infection and Drug Resistance 11:1645–58. doi: 10.2147/idr.s173867.
   PubMed Web of Science ®Google Scholar
• Atterbury, R. J., P. L. Connerton, C. E. Dodd, C. E. Rees, and I. F. Connerton. 2003. Application of host-specific bacteriophages to the surface of chicken skin leads to a reduction in recovery of Campylobacter jejuni. Applied and Environmental Microbiology 69 (10):6302–6. doi: 10.1128/AEM.69.10.6302-6306.2003.
   PubMed Web of Science ®Google Scholar
• Atterbury, R. J., M. A. Van Bergen, F. Ortiz, M. A. Lovell, J. A. Harris, A. De Boer, J. A. Wagenaar, V. M. Allen, and P. A. Barrow. 2007. Bacteriophage therapy to reduce Salmonella colonization of broiler chickens. Applied and Environmental Microbiology 73 (14):4543–9. doi: 10.1128/AEM.00049-07.
   PubMed Web of Science ®Google Scholar
• Bae, D., J.-W. Lee, J.-P. Chae, J.-W. Kim, J.-S. Eun, K.-W. Lee, and K.-H. Seo. 2021. Characterization of a novel bacteriophage φCJ22 and its prophylactic and inhibitory effects on necrotic enteritis and Clostridium perfringens in broilers. Poultry Science 100 (1):302–13. doi: 10.1016/j.psj.2020.10.019.
   PubMed Web of Science ®Google Scholar
• Bai, J., B. Jeon, and S. Ryu. 2019. Effective inhibition of Salmonella Typhimurium in fresh produce by a phage cocktail targeting multiple host receptors. Food Microbiology 77:52–60. doi: 10.1016/j.fm.2018.08.011.
   PubMed Web of Science ®Google Scholar
• Barbut, S. 2015. Live bird handling. The science of poultry and meat processing. University of Guelph, Guelph, Ontario, Canada.
   Google Scholar
• Barrow, P. A., and O. C. Freitas Neto. 2011. Pullorum disease and fowl typhoid-new thoughts on old diseases: A review. Avian Pathology 40 (1):1–13. doi: 10.1080/03079457.2010.542575.
   PubMed Web of Science ®Google Scholar
• Batinovic, S., F. Wassef, S. A. Knowler, D. T. F. Rice, C. R. Stanton, J. Rose, J. Tucci, T. Nittami, A. Vinh, G. R. Drummond, et al. 2019. Bacteriophages in natural and artificial environments. Pathogens 8 (3):100. doi: 10.3390/pathogens8030100.
   PubMed Web of Science ®Google Scholar
• Bigot, B., W. J. Lee, L. McIntyre, T. Wilson, J. A. Hudson, C. Billington, and J. A. Heinemann. 2011. Control of Listeria monocytogenes growth in a ready-to-eat poultry product using a bacteriophage. Food Microbiology 28 (8):1448–52. doi: 10.1016/j.fm.2011.07.001.
   PubMed Web of Science ®Google Scholar
• Bikel, S., A. Valdez-Lara, F. Cornejo-Granados, K. Rico, S. Canizales-Quinteros, X. Soberon, L. Del Pozo-Yauner, and A. Ochoa-Leyva. 2015. Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: Towards a systems-level understanding of human microbiome. Computational and Structural Biotechnology Journal 13:390–401. doi: 10.1016/j.csbj.2015.06.001.
   PubMed Web of Science ®Google Scholar
• Blasco, L., A. Ambroa, R. Trastoy, I. Bleriot, M. Moscoso, L. Fernández-Garcia, E. Perez-Nadales, F. Fernández-Cuenca, J. Torre-Cisneros, J. Oteo-Iglesias, et al. 2020. In vitro and in vivo efficacy of combinations of colistin and different endolysins against clinical strains of multi-drug resistant pathogens. Scientific Reports 10 (1):7163. doi: 10.1038/s41598-020-64145-7.
   PubMed Web of Science ®Google Scholar
• Blasdel, B., P. J. Ceyssens, and R. Lavigne. 2018. Preparing cDNA libraries from lytic phage-infected cells for whole transcriptome analysis by RNA-Seq. Methods in Molecular Biology (Clifton, N.J.) 1681:185–94. doi: 10.1007/978-1-4939-7343-9_14.
   PubMedGoogle Scholar
• Boon, M., D. Holtappels, C. Lood, V. van Noort, and R. Lavigne. 2020. Host range expansion of Pseudomonas virus LUZ7 Is driven by a conserved tail fiber mutation. PHAGE 1 (2):87–90. doi: 10.1089/phage.2020.0006.
   PubMedGoogle Scholar
• Borie, C., I. Albala, P. Sanchez, M. L. Sanchez, S. Ramirez, C. Navarro, M. A. Morales, A. J. Retamales, and J. Robeson. 2008. Bacteriophage treatment reduces Salmonella colonization of infected chickens. Avian Diseases 52 (1):64–7. doi: 10.1637/8091-082007-Reg.
   PubMed Web of Science ®Google Scholar
• Brives, C., and J. Pourraz. 2020. Phage therapy as a potential solution in the fight against AMR: Obstacles and possible futures. Palgrave Communications 6 (1):100. doi: 10.1057/s41599-020-0478-4.
   Web of Science ®Google Scholar
• Brovko, L. Y., H. Anany, and M. W. Griffiths. 2012. Bacteriophages for detection and control of bacterial pathogens in food and food-processing environment. Advances in Food and Nutrition Research 67:241–88. doi: 10.1016/b978-0-12-394598-3.00006-x.
   PubMedGoogle Scholar
• Brum, J. R., J. C. Ignacio-Espinoza, S. Roux, G. Doulcier, S. G. Acinas, A. Alberti, S. Chaffron, C. Cruaud, C. de Vargas, J. M. Gasol, et al. 2015. Ocean plankton. Patterns and ecological drivers of ocean viral communities. Science (New York, N.Y.) 348 (6237):1261498. doi: 10.1126/science.1261498.
   PubMed Web of Science ®Google Scholar
• Burmeister, A. R., A. Fortier, C. Roush, A. J. Lessing, R. G. Bender, R. Barahman, R. Grant, B. K. Chan, and P. E. Turner. 2020. Pleiotropy complicates a trade-off between phage resistance and antibiotic resistance. Proceedings of the National Academy of Sciences of the United States of America 117 (21):11207–16. doi: 10.1073/pnas.1919888117.
   PubMed Web of Science ®Google Scholar
• Bythwood, T. N., V. Soni, K. Lyons, A. Hurley-Bacon, M. D. Lee, C. Hofacre, S. Sanchez, and J. J. Maurer. 2019. Antimicrobial esistant Salmonella enterica Typhimurium colonizing chickens: The impact of plasmids, genotype, bacterial communities, and antibiotic administration on resistance. Frontiers in Sustainable Food Systems 3:20. doi: 10.3389/fsufs.2019.00020.
   Google Scholar
• Cadena, M., T. Kelman, M. L. Marco, and M. Pitesky. 2019. Understanding antimicrobial resistance (AMR) profiles of Salmonella biofilm and planktonic bacteria challenged with disinfectants commonly used during poultry processing. Foods (Basel, Switzerland) 8 (7):275. doi: 10.3390/foods8070275.
   PubMed Web of Science ®Google Scholar
• Caly, D. L., R. D’Inca, E. Auclair, and D. Drider. 2015. Alternatives to antibiotics to prevent necrotic enteritis in broiler chickens: A microbiologist’s perspective. Frontiers in Microbiology 6:1336. doi: 10.3389/fmicb.2015.01336.
   PubMed Web of Science ®Google Scholar
• Carrillo, L., C. R. J. Atterbury, A. el-Shibiny, P. L. Connerton, E. Dillon, A. Scott, and I. F. Connerton. 2005. Bacteriophage therapy to reduce Campylobacter jejuni colonization of broiler chickens. Applied and Environmental Microbiology 71 (11):6554–63. doi: 10.1128/AEM.71.11.6554-6563.2005.
   PubMed Web of Science ®Google Scholar
• Cartwright, E. J., K. A. Jackson, S. D. Johnson, L. M. Graves, B. J. Silk, and B. E. Mahon. 2013. Listeriosis outbreaks and associated food vehicles, United States, 1998–2008. Emerging Infectious Diseases 19 (1):1–9. doi: 10.3201/eid1901.120393.
   PubMed Web of Science ®Google Scholar
• Carvalho, C. M., B. W. Gannon, D. E. Halfhide, S. B. Santos, C. M. Hayes, J. M. Roe, and J. Azeredo. 2010. The in vivo efficacy of two administration routes of a phage cocktail to reduce numbers of Campylobacter coli and Campylobacter jejuni in chickens. BMC Microbiology 10 (1):1471–2180. doi: 10.1186/1471-2180-10-232.
   Google Scholar
• Centers for Disease Control and Prevention (CDC). 2020. Food and food animals. Retrieved from https://www.cdc.gov/drugresistance/food.html.
   Google Scholar
• Chatterjee, A., J. Willett, U. T. Nguyen, B. Monogue, K. Palmer, G. Dunny, and B. Duerkop. 2020. Parallel genomics uncover novel enterococcal-bacteriophage interactions. mBio 11 (2):e03120. doi: 10.1101/858506.
   PubMed Web of Science ®Google Scholar
• Chen, Y., H. Batra, J. Dong, C. Chen, V. B. Rao, and P. Tao. 2019. Genetic engineering of bacteriophages against infectious diseases. Frontiers in Microbiology 10:954. doi: 10.3389/fmicb.2019.00954.
   PubMed Web of Science ®Google Scholar
• Chibeu, A., L. Agius, A. Gao, P. M. Sabour, A. M. Kropinski, and S. Balamurugan. 2013. Efficacy of bacteriophage LISTEXP100 combined with chemical antimicrobials in reducing Listeria monocytogenes in cooked turkey and roast beef. International Journal of Food Microbiology 167 (2):208–14. doi: 10.1016/j.ijfoodmicro.2013.08.018.
   PubMed Web of Science ®Google Scholar
• Chinivasagam, H. N., W. Estella, L. Maddock, D. G. Mayer, C. Weyand, P. L. Connerton, and I. F. Connerton. 2020. Bacteriophages to control Campylobacter in commercially farmed broiler chickens, in Australia. Frontiers in Microbiology 11:632. doi: 10.3389/fmicb.2020.00632.
   PubMed Web of Science ®Google Scholar
• Cho, I.-H., and S. Ku. 2017. Current technical approaches for the early detection of foodborne pathogens: Challenges and opportunities. International Journal of Molecular Sciences 18 (10):2078. doi: 10.3390/ijms18102078.
   PubMed Web of Science ®Google Scholar
• Cieplak, T., N. Soffer, A. Sulakvelidze, and D. S. Nielsen. 2018. A bacteriophage cocktail targeting Escherichia coli reduces E. coli in simulated gut conditions, while preserving a non-targeted representative commensal normal microbiota. Gut Microbes 9 (5):391–9. doi: 10.1080/19490976.2018.1447291.
   PubMed Web of Science ®Google Scholar
• Clark, C. G., P. M. Chong, S. J. McCorrister, P. Simon, M. Walker, D. M. Lee, K. Nguy, K. Cheng, M. W. Gilmour, and G. R. Westmacott. 2014. The CJIE1 prophage of Campylobacter jejuni affects protein expression in growth media with and without bile salts. BMC Microbiology 14:70. doi: 10.1186/1471-2180-14-70.
   PubMed Web of Science ®Google Scholar
• Clavijo, V., D. Baquero, S. Hernandez, J. C. Farfan, J. Arias, A. Arévalo, P. Donado-Godoy, and M. Vives-Flores. 2019. Phage cocktail SalmoFREE reduces Salmonella on a commercial broiler farm. Poultry Science 98 (10):5054–63. doi: 10.3382/ps/pez251.
   PubMed Web of Science ®Google Scholar
• Collier, C. T., C. L. Hofacre, A. M. Payne, D. B. Anderson, P. Kaiser, R. I. Mackie, and H. R. Gaskins. 2008. Coccidia-induced mucogenesis promotes the onset of necrotic enteritis by supporting Clostridium perfringens growth. Veterinary Immunology and Immunopathology 122 (1–2):104–15. doi: 10.1016/j.vetimm.2007.10.014.
   PubMed Web of Science ®Google Scholar
• Colom, J., M. Cano-Sarabia, J. Otero, P. Cortés, D. Maspoch, and M. Llagostera. 2015. Liposome-encapsulated bacteriophages for enhanced oral phage therapy against Salmonella spp. Applied and Environmental Microbiology 81 (14):4841–9. doi: 10.1128/AEM.00812-15.
   PubMed Web of Science ®Google Scholar
• Comeau, A. M., F. Tétart, S. N. Trojet, M.-F. Prère, and H. M. Krisch. 2007. Phage-Antibiotic Synergy (PAS): beta-lactam and quinolone antibiotics stimulate virulent phage growth. PLoS One 2 (8):e799. doi: 10.1371/journal.pone.0000799.
   PubMed Web of Science ®Google Scholar
• Corcoran, M., D. Morris, N. De Lappe, J. O’Connor, P. Lalor, P. Dockery, and M. Cormican. 2014. Commonly used disinfectants fail to eradicate Salmonella enterica biofilms from food contact surface materials. Applied and Environmental Microbiology 80 (4):1507–14. doi: 10.1128/AEM.03109-13.
   PubMed Web of Science ®Google Scholar
• Costa, M. C., J. A. Bessegatto, A. A. Alfieri, J. S. Weese, J. A. B. Filho, and A. Oba. 2017. Different antibiotic growth promoters induce specific changes in the cecal microbiota membership of broiler chicken. PLoS One 12 (2):e0171642. doi: 10.1371/journal.pone.0171642.
   PubMed Web of Science ®Google Scholar
• Cucic, S., J. Lin, C. Khursigara, and H. Anany. 2019. Bacteriophages as biosanitizers: Using lytic phage to control and eradicate Listeria monocytogenes biofilm. Paper presented at the IAFP Annual Meeting.
   Google Scholar
• Dahshan, H., A. M. A. Merwad, and T. S. Mohamed. 2016. Listeria species in broiler poultry farms: Potential public health hazards. Journal of Microbiology and Biotechnology 26 (9):1551–6. doi: 10.4014/jmb.1603.03075.
   PubMed Web of Science ®Google Scholar
• Danovaro, R., C. Corinaldesi, A. Dell’anno, J. A. Fuhrman, J. J. Middelburg, R. T. Noble, and C. A. Suttle. 2011. Marine viruses and global climate change. FEMS Microbiology Reviews 35 (6):993–1034. doi: 10.1111/j.1574-6976.2010.00258.x.
   PubMed Web of Science ®Google Scholar
• Day, J. M., B. B. Oakley, B. S. Seal, and L. Zsak. 2015. Comparative analysis of the intestinal bacterial and RNA viral communities from sentinel birds placed on selected broiler chicken farms. PLoS One 10 (1):e0117210. doi: 10.1371/journal.pone.0117210.
   PubMed Web of Science ®Google Scholar
• Denes, T., H. C. den Bakker, J. I. Tokman, C. Guldimann, and M. Wiedmann. 2015. Selection and characterization of phage-resistant mutant strains of Listeria monocytogenes reveal host genes linked to phage adsorption. Applied and Environmental Microbiology 81 (13):4295–305. doi: 10.1128/AEM.00087-15.
   PubMed Web of Science ®Google Scholar
• Denyes, J. M., M. Dunne, S. Steiner, M. Mittelviefhaus, A. Weiss, H. Schmidt, J. Klumpp, and M. J. Loessner. 2017. Modified bacteriophage S16 long tail fiber proteins for rapid and specific immobilization and detection of Salmonella cells. Applied and Environmental Microbiology 83 (12):e00277-17. doi: 10.1128/AEM.00277-17.
   PubMed Web of Science ®Google Scholar
• Desdouits, M., M. de Graaf, S. Strubbia, B. B. Oude Munnink, A. Kroneman, F. S. Le Guyader, and M. P. G. Koopmans. 2020. Novel opportunities for NGS-based one health surveillance of foodborne viruses. One Health Outlook 2 (1):14. doi: 10.1186/s42522-020-00015-6.
   PubMedGoogle Scholar
• Devaney, R., J. Trudgett, A. Trudgett, C. Meharg, and V. Smyth. 2016. A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds. Avian Pathology 45 (6):616–29. doi: 10.1080/03079457.2016.1193123.
   PubMed Web of Science ®Google Scholar
• Devleesschauwer, B., M. Bouwknegt, M.-J J. Mangen, and A. H. Havelaar. 2017. Chapter 2 - Health and economic burden of Campylobacter. In Campylobacter, ed. G. Klein, 27–40. Cambridge, UK: Academic Press.
   Google Scholar
• Devoto, A. E., J. M. Santini, M. R. Olm, K. Anantharaman, P. Munk, J. Tung, E. A. Archie, P. J. Turnbaugh, K. D. Seed, R. Blekhman, et al. 2019. Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nature Microbiology 4 (4):693–700. doi: 10.1038/s41564-018-0338-9.
   PubMed Web of Science ®Google Scholar
• Diarra, M. S., and F. Malouin. 2014. Antibiotics in Canadian poultry productions and anticipated alternatives. Frontiers in Microbiology 5:282. doi: 10.3389/fmicb.2014.00282.
   PubMed Web of Science ®Google Scholar
• Dion, M. B., F. Oechslin, and S. Moineau. 2020. Phage diversity, genomics and phylogeny. Nature Reviews. Microbiology 18 (3):125–38. doi: 10.1038/s41579-019-0311-5.
   PubMed Web of Science ®Google Scholar
• Dufour, N., R. Delattre, J. D. Ricard, and L. Debarbieux. 2017. The lysis of pathogenic Escherichia coli by bacteriophages releases less endotoxin than by beta-lactams. Clinical Infectious Diseases 64 (11):1582–8. doi: 10.1093/cid/cix184.
   PubMed Web of Science ®Google Scholar
• Dugat-Bony, E., J. Lossouarn, M. De Paepe, A.-S. Sarthou, Y. Fedala, M.-A. Petit, and S. Chaillou. 2018. Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting virus-like particles. bioRxiv 2018:503599. doi: 10.1101/503599.
   Google Scholar
• Dundar, F., L. Skrabanek, and P. Zumbo. 2015. Introduction to differential gene expression analysis using RNA-seq. Cornell Workshops.
   Google Scholar
• Dunne, M., B. Rupf, M. Tala, X. Qabrati, P. Ernst, Y. Shen, E. Sumrall, L. Heeb, A. Plückthun, M. J. Loessner, et al. 2019. Reprogramming bacteriophage host range through structure-guided design of chimeric receptor binding proteins. Cell Reports 29 (5):1336–50.e4. doi: 10.1016/j.celrep.2019.09.062.
   PubMed Web of Science ®Google Scholar
• Edgar, R., M. McKinstry, J. Hwang, A. B. Oppenheim, R. A. Fekete, G. Giulian, C. Merril, K. Nagashima, and S. Adhya. 2006. High-sensitivity bacterial detection using biotin-tagged phage and quantum-dot nanocomplexes. Proceedings of the National Academy of Sciences of the United States of America 103 (13):4841–5. doi: 10.1073/pnas.0601211103.
   PubMed Web of Science ®Google Scholar
• Edwards, R. A., and F. Rohwer. 2005. Viral metagenomics. Nature Reviews. Microbiology 3 (6):504–10. doi: 10.1038/nrmicro1163.
   PubMed Web of Science ®Google Scholar
• El-Shibiny, A., A. Scott, A. Timms, Y. Metawea, P. Connerton, and I. Connerton. 2009. Application of a group II Campylobacter bacteriophage to reduce strains of Campylobacter jejuni and Campylobacter coli colonizing broiler chickens. Journal of Food Protection 72 (4):733–40. doi: 10.4315/0362-028x-72.4.733.
   PubMed Web of Science ®Google Scholar
• European Food Safety Authority (EFSA). 2015. The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2014. EFSA Journal 13 (12):4329. doi: 10.2903/j.efsa.2015.4329.
   Web of Science ®Google Scholar
• European Food Safety Authority (EFSA). 2019. The European Union one health 2018 zoonoses report. EFSA Journal 17 (12):e05926. doi: 10.2903/j.efsa.2019.5926.
   PubMed Web of Science ®Google Scholar
• Farenc, C., S. Spinelli, E. Vinogradov, D. Tremblay, S. Blangy, I. Sadovskaya, S. Moineau, and C. Cambillau. 2014. Molecular insights on the recognition of a Lactococcus lactis cell wall pellicle by the phage 1358 receptor binding protein. Journal of Virology 88 (12):7005–15. doi: 10.1128/JVI.00739-14.
   PubMed Web of Science ®Google Scholar
• Fernandes, E., V. C. Martins, C. Nobrega, C. M. Carvalho, F. A. Cardoso, S. Cardoso, J. Dias, D. Deng, L. D. Kluskens, P. P. Freitas, et al. 2014. A bacteriophage detection tool for viability assessment of Salmonella cells. Biosensors & Bioelectronics 52:239–46. doi: 10.1016/j.bios.2013.08.053.
   PubMed Web of Science ®Google Scholar
• Fiorentin, L., N. D. Vieira, and W. Barioni. Jr. 2005. Oral treatment with bacteriophages reduces the concentration of Salmonella Enteritidis PT4 in caecal contents of broilers. Avian Pathology : journal of the W.V.P.A 34 (3):258–63. doi: 10.1080/01445340500112157.
   PubMed Web of Science ®Google Scholar
• Food and Agriculture Organization (FAO). 2020a. Gateway to poultry production and products. http://www.fao.org/poultry-production-products/en/.
   Google Scholar
• Food and Agriculture Organization (FAO). 2020b. FAOSTAT. http://www.fao.org/faostat/en/#data/.
   Google Scholar
• Food Safety News (FSN). 2020. EU project uses phages to tackle Campylobacter in poultry. https://www.foodsafetynews.com/2020/11/eu-project-uses-phages-to-tackle-campylobacter-in-poultry/.
   Google Scholar
• Fortier, L. C., and O. Sekulovic. 2013. Importance of prophages to evolution and virulence of bacterial pathogens. Virulence 4 (5):354–65. doi: 10.4161/viru.24498.
   PubMed Web of Science ®Google Scholar
• Gambino, M., A. Nørgaard Sørensen, S. Ahern, G. Smyrlis, Y. E. Gencay, H. Hendrix, H. Neve, J.-P. Noben, R. Lavigne, and L. Brøndsted. 2020. Phage S144, a new polyvalent phage infecting Salmonella spp. and Cronobacter sakazakii. International Journal of Molecular Sciences 21 (15):5196. doi: 10.3390/ijms21155196.
   PubMedGoogle Scholar
• García, R., S. Latz, J. Romero, G. Higuera, K. García, and R. Bastías. 2019. Bacteriophage production models: An overview. Frontiers in Microbiology 10:1187. doi: 10.3389/fmicb.2019.01187.
   PubMed Web of Science ®Google Scholar
• Garner, M. R., K. E. James, M. C. Callahan, M. Wiedmann, and K. J. Boor. 2006. Exposure to salt and organic acids increases the ability of Listeria monocytogenes to invade Caco-2 cells but decreases its ability to survive gastric stress. Applied and Environmental Microbiology 72 (8):5384–95. doi: 10.1128/aem.00764-06.
   PubMed Web of Science ®Google Scholar
• Gencay, Y. E., M. C. H. Sørensen, C. Q. Wenzel, C. M. Szymanski, and L. Brøndsted. 2018. Phase variable expression of a single phage receptor in Campylobacter jejuni NCTC12662 influences sensitivity toward several diverse CPS-dependent phages. Frontiers in Microbiology 9:82. doi: 10.3389/fmicb.2018.00082.
   PubMed Web of Science ®Google Scholar
• Gerstmans, H., B. Criel, and Y. Briers. 2018. Synthetic biology of modular endolysins. Biotechnology Advances 36 (3):624–40. doi: 10.1016/j.biotechadv.2017.12.009.
   PubMed Web of Science ®Google Scholar
• Ghosh, D., A. G. Kohli, F. Moser, D. Endy, and A. M. Belcher. 2012. Refactored M13 bacteriophage as a platform for tumor cell imaging and drug delivery. ACS Synthetic Biology 1 (12):576–82. doi: 10.1021/sb300052u.
   PubMed Web of Science ®Google Scholar
• Gigante, A., and R. J. Atterbury. 2019. Veterinary use of bacteriophage therapy in intensively-reared livestock. Virology Journal 16 (1):1260. doi: 10.1186/s12985-019-1260-3.
   Web of Science ®Google Scholar
• González-Menéndez, E., L. Fernández, D. Gutiérrez, A. Rodríguez, B. Martínez, and P. García. 2018. Comparative analysis of different preservation techniques for the storage of Staphylococcus phages aimed for the industrial development of phage-based antimicrobial products. PLoS One 13 (10):e0205728. doi: 10.1371/journal.pone.0205728.
   PubMed Web of Science ®Google Scholar
• González-Mora, A., J. Hernández-Pérez, H. M. N. Iqbal, M. Rito-Palomares, and J. Benavides. 2020. Bacteriophage-based vaccines: A potent approach for antigen delivery. Vaccines 8 (3):504. doi: 10.3390/vaccines8030504.
   Web of Science ®Google Scholar
• Goode, D., V. M. Allen, and P. A. Barrow. 2003. Reduction of experimental Salmonella and Campylobacter contamination of chicken skin by application of lytic bacteriophages. Applied and Environmental Microbiology 69 (8):5032–6. doi: 10.1128/AEM.69.8.5032-5036.2003.
   PubMed Web of Science ®Google Scholar
• Grant, A., S. Parveen, J. Schwarz, F. Hashem, and B. Vimini. 2017. Reduction of Salmonella in ground chicken using a bacteriophage. Poultry Science 96 (8):2845–52. doi: 10.3382/ps/pex062.
   PubMed Web of Science ®Google Scholar
• Griffin, J. L., and A. Vidal-Puig. 2008. Current challenges in metabolomics for diabetes research: A vital functional genomic tool or just a ploy for gaining funding? Physiological Genomics 34 (1):1–5. doi: 10.1152/physiolgenomics.00009.2008.
   PubMed Web of Science ®Google Scholar
• Gu Liu, C., S. I. Green, L. Min, J. R. Clark, K. C. Salazar, A. L. Terwilliger, H. B. Kaplan, B. W. Trautner, R. F. Ramig, and A. W. Maresso. 2020. Phage-antibiotic synergy is driven by a unique combination of antibacterial mechanism of action and stoichiometry. mBio 11 (4):e01462-20. doi: 10.1128/mBio.01462-20.
   PubMed Web of Science ®Google Scholar
• Guenther, S., O. Herzig, L. Fieseler, J. Klumpp, and M. J. Loessner. 2012. Biocontrol of Salmonella Typhimurium in RTE foods with the virulent bacteriophage FO1-E2. International Journal of Food Microbiology 154 (1–2):66–72. doi: 10.1016/j.ijfoodmicro.2011.12.023.
   PubMed Web of Science ®Google Scholar
• Guenther, S., D. Huwyler, S. Richard, and M. J. Loessner. 2009. Virulent bacteriophage for efficient biocontrol of Listeria monocytogenes in ready-to-eat foods. Applied and Environmental Microbiology 75 (1):93–100. doi: 10.1128/AEM.01711-08.
   PubMed Web of Science ®Google Scholar
• Gurney, J., S. P. Brown, O. Kaltz, and M. E. Hochberg. 2020. Steering phages to combat bacterial pathogens. Trends in Microbiology 28 (2):85–94. doi: 10.1016/j.tim.2019.10.007.
   PubMed Web of Science ®Google Scholar
• Gutiérrez, D., L. Rodríguez-Rubio, B. Martínez, A. Rodríguez, and P. García. 2016. Bacteriophages as weapons against bacterial biofilms in the food industry. Frontiers in Microbiology 7:825. doi: 10.3389/fmicb.2016.00825.
   PubMed Web of Science ®Google Scholar
• Hagens, S., B. de Vegt, and R. Peterson. 2018. Efficacy of a commercial phage cocktail in reducing Salmonella contamination on poultry products- laboratory data and industrial trial data. Meat Muscle Biology 2 (2):2. doi: 10.221751/rmc2018.136.
   Google Scholar
• Hagens, S., and M. J. Loessner. 2010. Bacteriophage for biocontrol of foodborne pathogens: Calculations and considerations. Current Pharmaceutical Biotechnology 11 (1):58–68. doi: 10.2174/138920110790725429.
   PubMed Web of Science ®Google Scholar
• Hammerl, J. A., C. Jäckel, T. Alter, P. Janzcyk, K. Stingl, M. T. Knüver, and S. Hertwig. 2014. Reduction of Campylobacter jejuni in broiler chicken by successive application of group II and group III phages. PLoS One 9 (12):e114785. doi: 10.1371/journal.pone.0114785.
   PubMed Web of Science ®Google Scholar
• Handley, J. A., S. H. Park, S. A. Kim, and S. C. Ricke. 2018. Microbiome profiles of commercial broilers through evisceration and immersion chilling during poultry slaughter and the Identification of potential indicator microorganisms. Frontiers in Microbiology 9:345. doi: 10.3389/fmicb.2018.00345.
   PubMed Web of Science ®Google Scholar
• Hassan, A. Y., J. T. Lin, N. Ricker, and H. Anany. 2021. The age of phage: Friend or foe in the new dawn of therapeutic and biocontrol applications? Pharmaceuticals (Basel, Switzerland) 14 (3):199. doi: 10.3390/ph14030199.
   PubMedGoogle Scholar
• Hayes, S., J. Mahony, A. Nauta, and D. van Sinderen. 2017. Metagenomic approaches to assess bacteriophages in various environmental niches. Viruses 9 (6):127. doi: 10.3390/v9060127.
   PubMed Web of Science ®Google Scholar
• Hedman, H. D., K. A. Vasco, and L. Zhang. 2020. A review of antimicrobial resistance in poultry farming within low-resource settings. Animals 10 (8):1264. doi: 10.3390/ani10081264.
   Web of Science ®Google Scholar
• Hein, T. 2019. Antimicrobial reduction update. Canadian Poultry. https://www.canadianpoultrymag.com/antimicrobial-reduction-update-31145/.
   Google Scholar
• Hendrix, R. W., M. C. M. Smith, R. N. Burns, M. E. Ford, and G. F. Hatfull. 1999. Evolutionary relationships among diverse bacteriophages and prophages: All the world’s a phage. Proceedings of the National Academy of Sciences of the United States of America 96 (5):2192–7. doi: 10.1073/pnas.96.5.2192.
   PubMed Web of Science ®Google Scholar
• Hesse, S., M. Rajaure, E. Wall, J. Johnson, V. Bliskovsky, S. Gottesman, S. Adhya, and G. F. Hatfull. 2020. Phage resistance in multidrug-resistant Klebsiella pneumoniae ST258 evolves via diverse mutations that culminate in impaired adsorption. mBio 11 (1):e02530-19. doi: 10.1128/mBio.02530-19.
   PubMed Web of Science ®Google Scholar
• Higgins, J. P., S. E. Higgins, K. L. Guenther, W. Huff, A. M. Donoghue, D. J. Donoghue, and B. M. Hargis. 2005. Use of a specific bacteriophage treatment to reduce Salmonella in poultry products. Poultry Science 84 (7):1141–5. doi: 10.1093/ps/84.7.1141.
   PubMed Web of Science ®Google Scholar
• Hinkley, T. C., S. Singh, S. Garing, A. L. M. Le Ny, K. P. Nichols, J. E. Peters, J. N. Talbert, and S. R. Nugen. 2018. A phage-based assay for the rapid, quantitative, and single CFU visualization of E. coli (ECOR #13) in drinking water. Scientific Reports 8 (1):14630. doi: 10.1038/s41598-018-33097-4.
   PubMedGoogle Scholar
• Holtzman, T., R. Globus, S. Molshanski-Mor, A. Ben-Shem, I. Yosef, and U. Qimron. 2020. A continuous evolution system for ­contracting the host range of bacteriophage T7. Scientific Reports 10 (1):307. doi: 10.1038/s41598-019-57221-0.
   PubMed Web of Science ®Google Scholar
• Hong, Y., K. Schmidt, D. Marks, S. Hatter, A. Marshall, L. Albino, and P. Ebner. 2016. Treatment of Salmonella-contaminated eggs and pork with a broad-spectrum, single bacteriophage: Assessment of efficacy and resistance development. Foodborne Pathogens and Disease 13 (12):679–88. doi: 10.1089/fpd.2016.2172.
   PubMed Web of Science ®Google Scholar
• Howard-Varona, C., M. M. Lindback, G. E. Bastien, N. Solonenko, A. A. Zayed, H. Jang, B. Andreopoulos, H. M. Brewer, T. Glavina del Rio, J. N. Adkins, et al. 2020. Phage-specific metabolic reprogramming of virocells. The ISME Journal 14 (4):881–95. doi: 10.1038/s41396-019-0580-z.
   PubMed Web of Science ®Google Scholar
• Huff, W. E., G. R. Huff, N. C. Rath, and A. M. Donoghue. 2006. Evaluation of the influence of bacteriophage titer on the treatment of colibacillosis in broiler chickens. Poultry Science 85 (8):1373–7. doi: 10.1093/ps/85.8.1373.
   PubMed Web of Science ®Google Scholar
• Huff, W. E., G. R. Huff, N. C. Rath, J. M. Balog, and A. M. Donoghue. 2002. Prevention of Escherichia coli infection in broiler chickens with a bacteriophage aerosol spray. Poultry Science 81 (10):1486–91. doi: 10.1093/ps/81.10.1486.
   PubMed Web of Science ®Google Scholar
• Huff, W. E., G. R. Huff, N. C. Rath, J. M. Balog, and A. M. Donoghue. 2004. Therapeutic efficacy of bacteriophage and Baytril (enrofloxacin) individually and in combination to treat colibacillosis in broilers. Poultry Science 83 (12):1944–7. doi: 10.1093/ps/83.12.1944.
   PubMed Web of Science ®Google Scholar
• Huff, W. E., G. R. Huff, N. C. Rath, J. M. Balog, H. Xie, P. A. Moore, Jr., and A. M. Donoghue. 2002. Prevention of Escherichia coli respiratory infection in broiler chickens with bacteriophage (SPR02). Poultry Science 81 (4):437–41. doi: 10.1093/ps/81.4.437.
   PubMed Web of Science ®Google Scholar
• Hungaro, H. M., R. C. S. Mendonça, D. M. Gouvêa, M. C. D. Vanetti, and C. L. d. O. Pinto. 2013. Use of bacteriophages to reduce Salmonella in chicken skin in comparison with chemical agents. Food Research International (Ottawa, Ont.) 52 (1):75–81. doi: 10.1016/j.foodres.2013.02.032.
   Web of Science ®Google Scholar
• Huss, P., and S. Raman. 2020. Engineered bacteriophages as programmable biocontrol agents. Current Opinion in Biotechnology 61:116–21. doi: 10.1016/j.copbio.2019.11.013.
   PubMed Web of Science ®Google Scholar
• Intralytix Inc. 2014. ListShield. https://www.cfsanappsexternal.fda.gov/scripts/fdcc/index.cfm?set=GRASNotices&id=528.
   Google Scholar
• Islam, M. R., Y. I. Hassan, Q. Das, D. Lepp, M. Hernandez, D. V. Godfrey, S. Orban, K. Ross, P. Delaquis, and M. S. Diarra. 2020. Dietary organic cranberry pomace influences multiple blood biochemical parameters and cecal microbiota in pasture-raised broiler chickens. Journal of Functional Foods 72:104053. doi: 10.1016/j.jff.2020.104053.
   Web of Science ®Google Scholar
• Islam, M. R., D. Lepp, D. V. Godfrey, S. Orban, K. Ross, P. Delaquis, and M. S. Diarra. 2019. Effects of wild blueberry (Vaccinium angustifolium) pomace feeding on gut microbiota and blood metabolites in free-range pastured broiler chickens. Poultry Science 98 (9):3739–55. doi: 10.3382/ps/pez062.
   PubMed Web of Science ®Google Scholar
• Islam, M. S., Y. Zhou, L. Liang, I. Nime, K. Liu, T. Yan, X. Wang, and J. Li. 2019. Application of a phage cocktail for control of Salmonella in foods and reducing biofilms. Viruses 11 (9):841. doi: 10.3390/v11090:841.
   PubMed Web of Science ®Google Scholar
• Jäckel, C., J. A. Hammerl, and S. Hertwig. 2019. Campylobacter phage isolation and characterization: What we have learned so far. Methods and Protocols 2 (1):18. doi: 10.3390/mps2010018.
   PubMedGoogle Scholar
• Jain, S., K. Mukhopadhyay, and P. J. Thomassin. 2019. An economic analysis of Salmonella detection in fresh produce, poultry, and eggs using whole genome sequencing technology in Canada. Food Research International (Ottawa, Ont.) 116:802–9. doi: 10.1016/j.foodres.2018.09.014.
   PubMed Web of Science ®Google Scholar
• Jajere, S. M. 2019. A review of Salmonella enterica with particular focus on the pathogenicity and virulence factors, host specificity and antimicrobial resistance including multidrug resistance. Veterinary World 12 (4):504–21. doi: 10.14202/vetworld.2019.504-521.
   PubMed Web of Science ®Google Scholar
• Jepson, C. D., and J. B. March. 2004. Bacteriophage lambda is a highly stable DNA vaccine delivery vehicle. Vaccine 22 (19):2413–9. doi: 10.1016/j.vaccine.2003.11.065.
   PubMed Web of Science ®Google Scholar
• Jończyk, E., M. Kłak, R. Międzybrodzki, and A. Górski. 2011. The influence of external factors on bacteriophages—Review. Folia Microbiologica 56 (3):191–200. doi: 10.1007/s12223-011-0039-8.
   PubMed Web of Science ®Google Scholar
• Ju, Z., and W. Sun. 2017. Drug delivery vectors based on filamentous bacteriophages and phage-mimetic nanoparticles. Drug Delivery 24 (1):1898–908. doi: 10.1080/10717544.2017.1410259.
   PubMed Web of Science ®Google Scholar
• Kabir, S. M. L. 2010. Avian colibacillosis and salmonellosis: A closer look at epidemiology, pathogenesis, diagnosis, control and public health concerns. International Journal of Environmental Research and Public Health 7 (1):89–114. doi: 10.3390/ijerph7010089.
   PubMed Web of Science ®Google Scholar
• Kahn, L. H., G. Bergeron, M. W. Bourassa, B. De Vegt, J. Gill, F. Gomes, F. Malouin, K. Opengart, G. D. Ritter, R. S. Singer, et al. 2019. From farm management to bacteriophage therapy: Strategies to reduce antibiotic use in animal agriculture. Annals of the New York Academy of Sciences 1441 (1):31–9. doi: 10.1111/nyas.14034.
   PubMed Web of Science ®Google Scholar
• Kang, H. W., J. W. Kim, T. S. Jung, and G. J. Woo. 2013. wksl3, a New biocontrol agent for Salmonella enterica serovars enteritidis and typhimurium in foods: Characterization, application, sequence analysis, and oral acute toxicity study. Applied and Environmental Microbiology 79 (6):1956–68. doi: 10.1128/AEM.02793-12.
   PubMed Web of Science ®Google Scholar
• Karumathil, D. P., A. Upadhyay, and K. Venkitanarayanan. 2016. Antimicrobial packaging for poultry. Basel, Switzerland: Elsevier Inc.
   Google Scholar
• Kashiwagi, A., T. Kadoya, N. Kumasaka, T. Kumagai, F. S. Tsushima, and T. Yomo. 2018. Influence of adaptive mutations, from thermal adaptation experiments, on the infection cycle of RNA bacteriophage Qβ. Archives of Virology 163 (10):2655–62. doi: 10.1007/s00705-018-3895-6.
   PubMed Web of Science ®Google Scholar
• Kering, K. K., X. Zhang, R. Nyaruaba, J. Yu, and H. Wei. 2020. Application of adaptive evolution to improve the stability of bacteriophages during storage. Viruses 12 (4):423. doi: 10.3390/v12040423.
   PubMed Web of Science ®Google Scholar
• Kilcher, S., P. Studer, C. Muessner, J. Klumpp, M. J. Loessner, and S. Adhya. 2018. Cross-genus rebooting of custom-made, synthetic bacteriophage genomes in L-form bacteria. Proceedings of the National Academy of Sciences of the United States of America 115 (3):567–72. doi: 10.1073/pnas.1714658115.
   PubMed Web of Science ®Google Scholar
• Kim, K. H., G. Y. Lee, J. C. Jang, J. E. Kim, and Y. Y. Kim. 2013. Evaluation of anti-SE bacteriophage as feed additives to prevent Salmonella enteritidis (SE) in broiler. Asian-Australasian Journal of Animal Sciences 26 (3):386–93. doi: 10.5713/ajas.2012.12138.
   PubMed Web of Science ®Google Scholar
• Kittler, S., S. Fischer, A. Abdulmawjood, G. Glünder, and G. Klein. 2013. Effect of bacteriophage application on Campylobacter jejuni loads in commercial broiler flocks. Applied and Environmental Microbiology 79 (23):7525–33. doi: 10.1128/AEM.02703-13.
   PubMed Web of Science ®Google Scholar
• Knecht, L. E., M. Veljkovic, and L. Fieseler. 2020. Diversity and function of phage encoded depolymerases. Frontiers in Microbiology 10:2949. doi: 10.3389/fmicb.2019.02949.
   PubMed Web of Science ®Google Scholar
• Kretzer, J. W., R. Lehmann, M. Schmelcher, M. Banz, K.-P. Kim, C. Korn, and M. J. Loessner. 2007. Use of high-affinity cell wall-binding domains of bacteriophage endolysins for immobilization and separation of bacterial cells. Applied and Environmental Microbiology 73 (6):1992–2000. doi: 10.1128/aem.02402-06.
   PubMed Web of Science ®Google Scholar
• Kruk, Z. A., H. Yun, D. L. Rutley, E. J. Lee, Y. J. Kim, and C. Jo. 2011. The effect of high pressure on microbial population, meat quality and sensory characteristics of chicken breast fillet. Food Control 22 (1):6–12. doi: 10.1016/j.foodcont.2010.06.003.
   Web of Science ®Google Scholar
• Krysiak-Baltyn, K., G. J. O. Martin, and S. L. Gras. 2018. Computational modelling of large scale phage production using a two-stage batch process. Pharmaceuticals (Basel, Switzerland) 11 (2):31. doi: 10.3390/ph11020031.
   PubMedGoogle Scholar
• Kutter, E., D. Bryan, G. Ray, E. Brewster, B. Blasdel, and B. Guttman. 2018. From host to phage metabolism: Hot tales of phage T4’s takeover of E. coli. Viruses 10 (7):387. doi: 10.3390/v10070387.
   PubMed Web of Science ®Google Scholar
• Kwok, K. T. T., D. F. Nieuwenhuijse, M. V. T. Phan, and M. P. G. Koopmans. 2020. Virus metagenomics in farm animals: A systematic review. Viruses 12 (1):107. doi: 10.3390/v12010107.
   PubMed Web of Science ®Google Scholar
• Labonté, J. M., M. Pachiadaki, E. Fergusson, J. McNichol, A. Grosche, L. K. Gulmann, C. Vetriani, S. M. Sievert, and R. Stepanauskas. 2019. Single cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system. Frontiers in Microbiology 10:1262. doi: 10.3389/fmicb.2019.01262.
   PubMed Web of Science ®Google Scholar
• Lau, G. L., C. C. Sieo, W. S. Tan, M. Hair-Bejo, A. Jalila, and Y. W. Ho. 2010. Efficacy of a bacteriophage isolated from chickens as a therapeutic agent for colibacillosis in broiler chickens. Poultry Science 89 (12):2589–96. doi: 10.3382/ps.2010-00904.
   PubMed Web of Science ®Google Scholar
• Lee, W., A. Syed Atif, S. C. Tan, and C. H. Leow. 2017. Insights into the chicken IgY with emphasis on the generation and applications of chicken recombinant monoclonal antibodies. Journal of Immunological Methods 447:71–85. doi: 10.1016/j.jim.2017.05.001.
   PubMed Web of Science ®Google Scholar
• Leekha, S., C. L. Terrell, and R. S. Edson. 2011. General principles of antimicrobial therapy. Mayo Clinic Proceedings 86 (2):156–67. doi: 10.4065/mcp.2010.0639.
   PubMed Web of Science ®Google Scholar
• Legrand, P., B. Collins, S. Blangy, J. Murphy, S. Spinelli, C. Gutierrez, N. Richet, C. Kellenberger, A. Desmyter, J. Mahony, et al. 2016. The atomic structure of the phage Tuc2009 baseplate tripod suggests that host recognition involves two different carbohydrate binding modules. mBio 7 (1):e01781-15. doi: 10.1128/mBio.01781-15.
   PubMed Web of Science ®Google Scholar
• Lemay, M.-L., A. Otto, S. Maaß, K. Plate, D. Becher, and S. Moineau. 2019. Investigating Lactococcus lactis MG1363 response to phage p2 infection at the proteome level. Molecular & Cellular Proteomics 18 (4):704–14. doi: 10.1074/mcp.RA118.001135.
   PubMed Web of Science ®Google Scholar
• Li, M., H. Lin, Y. Jing, and J. Wang. 2020. Broad-host-range Salmonella bacteriophage STP4-a and its potential application evaluation in poultry industry. Poultry Science 99 (7):3643–54. doi: 10.1016/j.psj.2020.03.051.
   PubMed Web of Science ®Google Scholar
• Liang, Y., L. Wang, Z. Wang, J. Zhao, Q. Yang, M. Wang, K. Yang, L. Zhang, N. Jiao, and Y. Zhang. 2019. Metagenomic analysis of the diversity of DNA viruses in the surface and deep sea of the south China sea. Frontiers in Microbiology 10:1951. doi: 10.3389/fmicb.2019.01951.
   PubMed Web of Science ®Google Scholar
• Lim, T.-H., D.-H. Lee, Y.-N. Lee, J.-K. Park, H.-N. Youn, M.-S. Kim, H.-J. Lee, S.-Y. Yang, Y.-W. Cho, J.-B. Lee, et al. 2011. Efficacy of bacteriophage therapy on horizontal transmission of Salmonella Gallinarum on commercial layer chickens. Avian Diseases 55 (3):435–8. doi: 10.1637/9599-111210-Reg.1.
   PubMed Web of Science ®Google Scholar
• Lima, D. A., S. P. Cibulski, F. Finkler, T. F. Teixeira, A. P. M. Varela, C. Cerva, M. R. Loiko, C. M. Scheffer, H. F. Dos Santos, F. Q. Mayer, et al. 2017. Faecal virome of healthy chickens reveals a large diversity of the eukaryote viral community, including novel circular ssDNA viruses. Journal of General Virology 98 (4):690–703. doi: 10.1099/jgv.0.000711.
   PubMed Web of Science ®Google Scholar
• Liu, Y., Q. Gong, X. Qian, D. Li, H. Zeng, Y. Li, F. Xue, J. Ren, X. Zhu Ge, F. Tang, et al. 2020. Prophage phiv205-1 facilitates biofilm formation and pathogenicity of avian pathogenic Escherichia coli strain DE205B. Veterinary Microbiology 247:108752. doi: 10.1016/j.vetmic.2020.108752.
   PubMed Web of Science ®Google Scholar
• Locatelli, A., M. A. Lewis, and M. J. Rothrock. 2017. The distribution of Listeria in pasture-raised broiler farm soils Is potentially related to University of Vermont medium enrichment bias toward Listeria innocua over Listeria monocytogenes. Frontiers in Veterinary Science 4:227. doi: 10.3389/fvets.2017.00227.
   PubMed Web of Science ®Google Scholar
• Lone, A., H. Anany, M. Hakeem, L. Aguis, A.-C. Avdjian, M. Bouget, A. Atashi, L. Brovko, D. Rochefort, and M. W. Griffiths. 2016. Development of prototypes of bioactive packaging materials based on immobilized bacteriophages for control of growth of bacterial pathogens in foods. International Journal of Food Microbiology 217:49–58. doi: 10.1016/j.ijfoodmicro.2015.10.011.
   PubMed Web of Science ®Google Scholar
• Lood, C., K. Danis-Wlodarczyk, B. G. Blasdel, H. B. Jang, D. Vandenheuvel, Y. Briers, J.-P. Noben, V. van Noort, Z. Drulis-Kawa, and R. Lavigne. 2020. Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages. Environmental Microbiology 22 (6):2165–81. doi: 10.1111/1462-2920.14979.
   PubMed Web of Science ®Google Scholar
• Lowe, R., N. Shirley, M. Bleackley, S. Dolan, and T. Shafee. 2017. Transcriptomics technologies. PLoS Computational Biology 13 (5):e1005457. doi: 10.1371/journal.pcbi.1005457.
   PubMed Web of Science ®Google Scholar
• Lu, T. K., and J. J. Collins. 2007. Dispersing biofilms with engineered enzymatic bacteriophage. Proceedings of the National Academy of Sciences of the United States of America 104 (27):11197–202. doi: 10.1073/pnas.0704624104.
   PubMed Web of Science ®Google Scholar
• Ma, Y., J. C. Pacan, Q. Wang, Y. Xu, X. Huang, A. Korenevsky, and P. M. Sabour. 2008. Microencapsulation of bacteriophage felix O1 into chitosan-alginate microspheres for oral delivery. Applied and Environmental Microbiology 74 (15):4799–805. doi: 10.1128/AEM.00246-08.
   PubMed Web of Science ®Google Scholar
• Mahony, J., O. McAuliffe, R. P. Ross, and D. van Sinderen. 2011. Bacteriophages as biocontrol agents of food pathogens. Current Opinion in Biotechnology 22 (2):157–63. doi: 10.1016/j.copbio.2010.10.008.
   PubMed Web of Science ®Google Scholar
• Marinelli, L. J., G. F. Hatfull, and M. Piuri. 2012. Recombineering: A powerful tool for modification of bacteriophage genomes. Bacteriophage 2 (1):5–14. doi: 10.4161/bact.18778.
   PubMed Web of Science ®Google Scholar
• Marotta, F., G. Garofolo, L. D. Marcantonio, G. Di Serafino, D. Neri, R. Romantini, L. Sacchini, A. Alessiani, G. Di Donato, R. Nuvoloni, et al. 2019. Antimicrobial resistance genotypes and phenotypes of Campylobacter jejuni isolated in Italy from humans, birds from wild and urban habitats, and poultry. PLoS One 14 (10):e0223804. doi: 10.1371/journal.pone.0223804.
   PubMed Web of Science ®Google Scholar
• Matin, M. A., M. A. Islam, and M. M. Khatun. 2017. Prevalence of colibacillosis in chickens in greater Mymensingh district of Bangladesh. Veterinary World 10 (1):29–33. doi: 10.14202/vetworld.2017.29-33.
   PubMed Web of Science ®Google Scholar
• Maung, A. T., T. N. Mohammadi, S. Nakashima, P. Liu, Y. Masuda, K. i Honjoh, and T. Miyamoto. 2019. Antimicrobial resistance profiles of Listeria monocytogenes isolated from chicken meat in Fukuoka, Japan. International Journal of Food Microbiology 304:49–57. doi: 10.1016/j.ijfoodmicro.2019.05.016.
   PubMed Web of Science ®Google Scholar
• McLean, J. S., and R. S. Lasken. 2014. Single cell genomics of bacterial pathogens: Outlook for infectious disease research. Genome Medicine 6 (11):108. doi: 10.1186/s13073-014-0108-0.
   PubMedGoogle Scholar
• Medzhitov, R. 2007. Recognition of microorganisms and activation of the immune response. Nature 449 (7164):819–26. doi: 10.1038/nature06246.
   PubMed Web of Science ®Google Scholar
• Mehdi, Y., M.-P. Létourneau-Montminy, M.-L. Gaucher, Y. Chorfi, G. Suresh, T. Rouissi, S. K. Brar, C. Côté, A. A. Ramirez, and S. Godbout. 2018. Use of antibiotics in broiler production: Global impacts and alternatives. Animal Nutrition 4 (2):170–8. doi: 10.1016/j.aninu.2018.03.002.
   Web of Science ®Google Scholar
• Meile, S., S. Kilcher, M. J. Loessner, and M. Dunne. 2020. Reporter phage-based detection of bacterial pathogens: Design guidelines and recent developments. Viruses 12 (9):944. doi: 10.3390/v12090944.
   PubMed Web of Science ®Google Scholar
• Meile, S., A. Sarbach, J. Du, M. Schuppler, C. Saez, M. J. Loessner, and S. Kilcher. 2020. Engineered reporter phages for rapid bioluminescence-based detection and differentiation of viable Listeria cells. Applied and Environmental Microbiology 86 (11):e00442-20. doi: 10.1128/AEM.00442-20.
   PubMed Web of Science ®Google Scholar
• Micciche, A. C., M. J. Rothrock, Jr., Y. Yang, and S. C. Ricke. 2019. Essential oils as an intervention strategy to reduce Campylobacter in poultry production: A review. Frontiers in Microbiology 10:1058. doi: 10.3389/fmicb.2019.01058.
   PubMed Web of Science ®Google Scholar
• Micciche, A. C., P. M. Rubinelli, and S. C. Ricke. 2018. Source of water and potential sanitizers and biological antimicrobials for alternative poultry processing food safety applications. Frontiers in Sustainable Food Systems 2:82. doi: 10.3389/fsufs.2018.00082.
   Google Scholar
• Miki, T., T. Nakazawa, T. Yokokawa, and T. Nagata. 2008. Functional consequences of viral impacts on bacterial communities: A food-web model analysis. Freshwater Biology 53 (6):1142–53. doi: 10.1111/j.1365-2427.2007.01934.x.
   Web of Science ®Google Scholar
• Miller, R. W., E. J. Skinner, A. Sulakvelidze, G. F. Mathis, and C. L. Hofacre. 2010. Bacteriophage therapy for control of necrotic enteritis of broiler chickens experimentally infected with Clostridium perfringens. Avian Diseases 54 (1):33–40. doi: 10.1637/8953-060509-Reg.1.
   PubMed Web of Science ®Google Scholar
• Minot, S., R. Sinha, J. Chen, H. Li, S. A. Keilbaugh, G. D. Wu, J. D. Lewis, and F. D. Bushman. 2011. The human gut virome: Inter-individual variation and dynamic response to diet. Genome Research 21 (10):1616–25. doi: 10.1101/gr.122705.111.
   PubMed Web of Science ®Google Scholar
• Montañez-Izquierdo, V. Y., D. I. Salas-Vázquez, and J. J. Rodríguez-Jerez. 2012. Use of epifluorescence microscopy to assess the effectiveness of phage P100 in controlling Listeria monocytogenes biofilms on stainless steel surfaces. Food Control 23 (2):470–7. doi: 10.1016/j.foodcont.2011.08.016.
   Web of Science ®Google Scholar
• Mottet, A., and G. Tempio. 2017. Global poultry production: Current state and future outlook and challenges. World’s Poultry Science Journal 73 (2):245–56. doi: 10.1017/s0043933917000071.
   Web of Science ®Google Scholar
• Moye, Z. D., J. Woolston, and A. Sulakvelidze. 2018. Bacteriophage applications for food production and processing. Viruses 10 (4):205–22. doi: 10.3390/v10040205.
   PubMed Web of Science ®Google Scholar
• Naghizadeh, M., M. A. Karimi Torshizi, S. Rahimi, and T. S. Dalgaard. 2019. Synergistic effect of phage therapy using a cocktail rather than a single phage in the control of severe colibacillosis in quails. Poultry Science 98 (2):653–63. doi: 10.3382/ps/pey414.
   PubMed Web of Science ®Google Scholar
• Nair, D. V. T., K. Venkitanarayanan, and A. K. Johny. 2018. Antibiotic-resistant Salmonella in the food supply and the potential role of antibiotic alternatives for control. Foods 7 (10):167. doi: 10.3390/foods7100167.
   PubMed Web of Science ®Google Scholar
• National Center for Biotechnology Information (NCBI). 2021. https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239&host=bacteria. Accessed January 14, 2021.
   Google Scholar
• Nhung, N. T., N. Chansiripornchai, and J. J. Carrique-Mas. 2017. Antimicrobial resistance in bacterial poultry pathogens: A review. Frontiers in Veterinary Science 4:1–17. doi: 10.3389/fvets.2017.00126.
   PubMed Web of Science ®Google Scholar
• Nicastro, J., K. Sheldon, and R. A. Slavcev. 2014. Bacteriophage lambda display systems: Developments and applications. Applied Microbiology and Biotechnology 98 (7):2853–66. doi: 10.1007/s00253-014-5521-1.
   PubMed Web of Science ®Google Scholar
• Niu, Y. D., T. A. McAllister, Y. Xu, R. P. Johnson, T. P. Stephens, and K. Stanford. 2009. Prevalence and impact of bacteriophages on the presence of Escherichia coli O157:H7 in feedlot cattle and their environment. Applied and Environmental Microbiology 75 (5):1271–8. doi: 10.1128/AEM.02100-08.
   PubMed Web of Science ®Google Scholar
• Nobrega, F. L., A. R. Costa, J. F. Santos, M. F. Siliakus, J. W. M. van Lent, S. W. M. Kengen, J. Azeredo, and L. D. Kluskens. 2016. Genetically manipulated phages with improved pH resistance for oral administration in veterinary medicine. Scientific Reports 6 (1):39235. doi: 10.1038/srep39235.
   PubMedGoogle Scholar
• Oda, M., M. Morita, H. Unno, and Y. Tanji. 2004. Rapid detection of Escherichia coli O157:H7 by using green fluorescent protein-labeled PP01 bacteriophage. Applied and Environmental Microbiology 70 (1):527–34. doi: 10.1128/AEM.70.1.527-534.2004.
   PubMed Web of Science ®Google Scholar
• Organisation for Economic Co-operation and Development (OECD). 2020. Meat consumption (indicator). https://data.oecd.org/agroutput/meat-consumption.htm.
   Google Scholar
• Oechslin, F. 2018. Resistance development to bacteriophages occurring during bacteriophage therapy. Viruses 10 (7):351. doi: 10.3390/v10070351.
   PubMed Web of Science ®Google Scholar
• Oliveira, A., R. Sereno, and J. Azeredo. 2010. In vivo efficiency evaluation of a phage cocktail in controlling severe colibacillosis in confined conditions and experimental poultry houses. Veterinary Microbiology 146 (3–4):303–8. doi: 10.1016/j.vetmic.2010.05.015.
   PubMed Web of Science ®Google Scholar
• Oliveira, H., V. Thiagarajan, M. Walmagh, S. Sillankorva, R. Lavigne, M. T. Neves-Petersen, L. D. Kluskens, and J. Azeredo. 2014. A thermostable Salmonella phage endolysin, Lys68, with broad bactericidal properties against gram-negative pathogens in presence of weak acids. PLoS One 9 (10):e108376. doi: 10.1371/journal.pone.0108376.
   PubMed Web of Science ®Google Scholar
• Oosterik, L. H., H. N. Tuntufye, J. Tsonos, T. Luyten, S. Noppen, S. Liekens, R. Lavigne, P. Butaye, and B. M. Goddeeris. 2016. Bioluminescent avian pathogenic Escherichia coli for monitoring colibacillosis in experimentally infected chickens. Veterinary Journal (London, England : 1997) 216:87–92. doi: 10.1016/j.tvjl.2016.07.011.
   PubMed Web of Science ®Google Scholar
• Orquera, S., G. Gölz, S. Hertwig, J. Hammerl, D. Sparborth, A. Joldic, and T. Alter. 2012. Control of Campylobacter spp. and Yersinia enterocolitica by virulent bacteriophages. Journal of Molecular and Genetic Medicine 6:273–8. doi: 10.4172/1747-0862.1000049.
   PubMedGoogle Scholar
• Paez-Espino, D., I. A. Chen, K. Palaniappan, A. Ratner, K. Chu, E. Szeto, M. Pillay, J. Huang, V. M. Markowitz, T. Nielsen, et al. 2017. IMG/VR: A database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Research 45 (D1):D457–65. doi: 10.1093/nar/gkw1030.
   PubMed Web of Science ®Google Scholar
• Parmar, K. M., S. L. Gaikwad, P. K. Dhakephalkar, R. Kothari, and R. P. Singh. 2017. Intriguing interaction of bacteriophage-host ­association: An understanding in the era of omics. Frontiers in Microbiology 8:559. doi: 10.3389/fmicb.2017.00559.
   PubMed Web of Science ®Google Scholar
• Perera, M. N., T. Abuladze, M. Li, J. Woolston, and A. Sulakvelidze. 2015. Bacteriophage cocktail significantly reduces or eliminates Listeria monocytogenes contamination on lettuce, apples, cheese, smoked salmon and frozen foods. Food Microbiology 52:42–8. doi: 10.1016/j.fm.2015.06.006.
   PubMed Web of Science ®Google Scholar
• Phagelux Inc. 2020. SalmoPro. https://www.fda.gov/media/95017/download.
   Google Scholar
• Public Health Agency of Canada (PHAC). 2019. Public Health Notice - Outbreak of Listeria infections linked to Rosemount brand cooked diced chicken. https://www.newswire.ca/news-releases/public-health-notice-outbreak-of-listeria-infections-linked-to-rosemount-brand-cooked-diced-chicken-835486323.html.
   Google Scholar
• Public Health England (PHE). 2016. Antimicrobial resistance in Campylobacter jejuni and Campylobacter coli from retail chilled chicken in the UK (9789512947188). https://www.doria.fi/bitstream/handle/10024/70812/AnnalesD976Lehtopolku.pdf?sequence=1#LehtopolkuB5.indd:.7777.
   Google Scholar
• Philipson, C. W., L. J. Voegtly, M. R. Lueder, K. A. Long, G. K. Rice, K. G. Frey, B. Biswas, R. Z. Cer, T. Hamilton, and K. A. Bishop-Lilly. 2018. Characterizing phage genomes for therapeutic applications. Viruses 10 (4):188. doi: 10.3390/v10040188.
   PubMed Web of Science ®Google Scholar
• Pires, D. P., H. Oliveira, L. D. R. Melo, S. Sillankorva, and J. Azeredo. 2016. Bacteriophage-encoded depolymerases: Their diversity and biotechnological applications. Applied Microbiology and Biotechnology 100 (5):2141–51. doi: 10.1007/s00253-015-7247-0.
   PubMed Web of Science ®Google Scholar
• Polaska, M., and B. Sokolowska. 2019. Bacteriophages-a new hope or a huge problem in the food industry. AIMS Microbiology 5 (4):324–46. doi: 10.3934/microbiol.2019.4.324.
   PubMed Web of Science ®Google Scholar
• Proteon Pharmaceut. 2020. Bafasal. https://www.proteonpharma.com/products/bafasal-poultry/.
   Google Scholar
• Rabinovich, L., N. Sigal, I. Borovok, R. Nir-Paz, and A. A. Herskovits. 2012. Prophage excision activates Listeria competence genes that promote phagosomal escape and virulence. Cell 150 (4):792–802. doi: 10.1016/j.cell.2012.06.036.
   PubMed Web of Science ®Google Scholar
• Ramirez, K., C. Cazarez-Montoya, H. S. Lopez-Moreno, and N. Castro-del Campo. 2018. Bacteriophage cocktail for biocontrol of Escherichia coli O157:H7: Stability and potential allergenicity study. PLoS One 13 (5):e0195023. doi: 10.1371/journal.pone.0195023.
   PubMed Web of Science ®Google Scholar
• Richards, P. J., P. L. Connerton, and I. F. Connerton. 2019. Phage biocontrol of Campylobacter jejuni in chickens does not produce collateral effects on the gut microbiota. Frontiers in Microbiology 10:476. doi: 10.3389/fmicb.2019.00476.
   PubMed Web of Science ®Google Scholar
• Rodríguez-Rubio, L., B. Martínez, D. M. Donovan, A. Rodríguez, and P. García. 2013. Bacteriophage virion-associated peptidoglycan hydrolases: Potential new enzybiotics. Critical Reviews in Microbiology 39 (4):427–34. doi: 10.3109/1040841X.2012.723675.
   PubMed Web of Science ®Google Scholar
• Rosenquist, H., L. Boysen, A. L. Krogh, A. N. Jensen, and M. Nauta. 2013. Campylobacter contamination and the relative risk of illness from organic broiler meat in comparison with conventional broiler meat. International Journal of Food Microbiology 162 (3):226–30. doi: 10.1016/j.ijfoodmicro.2013.01.022.
   PubMed Web of Science ®Google Scholar
• Ross, A., S. Ward, and P. Hyman. 2016. More is better: Selecting for broad host range bacteriophages. Frontiers in Microbiology 7:1352. doi: 10.3389/fmicb.2016.01352.
   PubMed Web of Science ®Google Scholar
• Rothrock, M. J., A. C. Micciche, A. R. Bodie, and S. C. Ricke. 2019. Listeria occurrence and potential control strategies in alternative and conventional poultry processing and retail. Frontiers in Sustainable Food Systems 3:33. doi: 10.3389/fsufs.2019.00033.
   Google Scholar
• Rouger, A., O. Tresse, and M. Zagorec. 2017. Bacterial contaminants of poultry meat: Sources, species, and dynamics. Microorganisms 5 (3):50. doi: 10.3390/microorganisms5030050.
   PubMed Web of Science ®Google Scholar
• Roux, S., E. M. Adriaenssens, B. E. Dutilh, E. V. Koonin, A. M. Kropinski, M. Krupovic, J. H. Kuhn, R. Lavigne, J. R. Brister, A. Varsani, et al. 2019. Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature Biotechnology 37 (1):29–37. doi: 10.1038/nbt.4306.
   PubMed Web of Science ®Google Scholar
• Rustad, M., A. Eastlund, P. Jardine, and V. Noireaux. 2018. Cell-free TXTL synthesis of infectious bacteriophage T4 in a single test tube reaction. Synthetic Biology (Oxford, England) 3 (1):ysy002. doi: 10.1093/synbio/ysy002.
   PubMedGoogle Scholar
• Sacher, J. C., A. Flint, J. Butcher, B. Blasdel, H. M. Reynolds, R. Lavigne, A. Stintzi, and C. M. Szymanski. 2018. Transcriptomic analysis of the Campylobacter jejuni response to T4-Like phage NCTC 12673 infection. Viruses 10 (6):332. doi: 10.3390/v10060332.
   PubMed Web of Science ®Google Scholar
• Sacher, J. C., A. Shajahan, J. Butcher, R. T. Patry, A. Flint, D. R. Hendrixson, A. Stintzi, P. Azadi, and C. M. Szymanski. 2020. Binding of phage-encoded FlaGrab to motile Campylobacter jejuni flagella Inhibits growth, downregulates energy metabolism, and requires specific flagellar glycans. Frontiers in Microbiology 11:397. doi: 10.3389/fmicb.2020.00397.
   PubMed Web of Science ®Google Scholar
• Sarhan, W. A., and H. M. Azzazy. 2015. Phage approved in food, why not as a therapeutic? Expert Review of anti-Infective Therapy 13 (1):91–101. doi: 10.1586/14787210.2015.990383.
   PubMed Web of Science ®Google Scholar
• Sartorius, R., L. D’Apice, A. Prisco, and P. De Berardinis. 2019. Arming filamentous bacteriophage, a nature-made nanoparticle, for new vaccine and immunotherapeutic strategies. Pharmaceutics 11 (9):437. doi: 10.3390/pharmaceutics11090437.
   PubMed Web of Science ®Google Scholar
• Sartorius, R., D. Russo, L. D’Apice, P. De Berardinis, and P. Berardinis. 2012. Innovation in vaccinology. In Filamentous bacteriophages: An antigen and gene delivery system, 123–34. Berlin/Heidelberg, Germany: Springer Science and Business Media LLC.
   Google Scholar
• Scallan, E., S. M. Crim, A. Runkle, O. L. Henao, B. E. Mahon, R. M. Hoekstra, and P. M. Griffin. 2015. Bacterial enteric infections among older adults in the United States: Foodborne Diseases Active Surveillance Network, 1996–2012. Foodborne Pathogens and Disease 12 (6):492–9. doi: 10.1089/fpd.2014.1915.
   PubMed Web of Science ®Google Scholar
• Schwanhäusser, B., D. Busse, N. Li, G. Dittmar, J. Schuchhardt, J. Wolf, W. Chen, and M. Selbach. 2011. Global quantification of mammalian gene expression control. Nature 473 (7347):337–42. doi: 10.1038/nature10098.
   PubMed Web of Science ®Google Scholar
• Shang, Y., S. Kumar, B. Oakley, and W. K. Kim. 2018. Chicken gut microbiota: Importance and detection technology. Frontiers in Veterinary Science 5:254. doi: 10.3389/fvets.2018.00254.
   PubMed Web of Science ®Google Scholar
• Shi, Z., M. J. Rothrock, Jr., and S. C. Ricke. 2019. Applications of microbiome analyses in alternative poultry broiler production systems. Frontiers in Veterinary Science 6:157. doi: 10.3389/fvets.2019.00157.
   PubMed Web of Science ®Google Scholar
• Shivaprasad, H. L. 2000. Fowl typhoid and pullorum disease. Revue Scientifique et Technique (International Office of Epizootics) 19 (2):405–24. doi: 10.20506/rst.19.2.1222.
   PubMed Web of Science ®Google Scholar
• Shkoporov, A. N., and C. Hill. 2019. Bacteriophages of the human gut: The “known unknown” of the microbiome. Cell Host & Microbe 25 (2):195–209. doi: 10.1016/j.chom.2019.01.017.
   PubMed Web of Science ®Google Scholar
• Sillankorva, S. M., H. Oliveira, and J. Azeredo. 2012. Bacteriophages and their role in food safety. International Journal of Microbiology 2012 (10):863945. doi: 10.1155/2012/863945.
   PubMedGoogle Scholar
• Siringan, P., P. L. Connerton, R. J. Payne, and I. F. Connerton. 2011. Bacteriophage-mediated dispersal of Campylobacter jejuni biofilms. Applied and Environmental Microbiology 77 (10):3320–6. doi: 10.1128/AEM.02704-10.
   PubMed Web of Science ®Google Scholar
• Sklar, I. B., and R. D. Joerger. 2001. Attempts to utilize bacteriophage to combat Salmonella enterica serovar Entemtidis infection in chickens. Journal of Food Safety 21 (1):15–29. doi: 10.1111/j.1745-4565.2001.tb00305.x.
   Web of Science ®Google Scholar
• Skovgaard, N. 2010. Salmonella and Campylobacter in chicken meat, Meeting report, Microbiological Risk Assessment Series 19. International Journal of Food Microbiology 144 (1):208. doi: 10.1016/j.ijfoodmicro.2010.09.004.
   Google Scholar
• Sommer, J., C. Trautner, A. K. Witte, S. Fister, D. Schoder, P. Rossmanith, and P. J. Mester. 2019. Don’t shut the stable door after the phage has bolted-The importance of bacteriophage inactivation in food environments. Viruses 11 (5):468. doi: 10.3390/v11050468.
   PubMed Web of Science ®Google Scholar
• Spain, C. V., D. Freund, H. Mohan-Gibbons, R. G. Meadow, and L. Beacham. 2018. Are they buying it? United States consumers’ changing attitudes toward more humanely raised meat, eggs, and dairy. Animals 8 (8):128. doi: 10.3390/ani8080128.
   Web of Science ®Google Scholar
• Spricigo, D. A., C. Bardina, P. Cortes, and M. Llagostera. 2013. Use of a bacteriophage cocktail to control Salmonella in food and the food industry. International Journal of Food Microbiology 165 (2):169–74. doi: 10.1016/j.ijfoodmicro.2013.05.009.
   PubMed Web of Science ®Google Scholar
• Srey, S., I. K. Jahid, and S. D. Ha. 2013. Biofilm formation in food industries: A food safety concern. Food Control 31 (2):572–85. doi: 10.1016/j.foodcont.2012.12.001.
   Web of Science ®Google Scholar
• Stanford, K., T. A. McAllister, Y. D. Niu, T. P. Stephens, A. Mazzocco, T. E. Waddell, and R. P. Johnson. 2010. Oral delivery systems for encapsulated bacteriophages targeted at Escherichia coli O157:H7 in feedlot cattle. Journal of Food Protection 73 (7):1304–12. doi: 10.4315/0362-028X-73.7.1304.
   PubMed Web of Science ®Google Scholar
• Sukumaran, A. T., R. Nannapaneni, A. Kiess, and C. S. Sharma. 2015. Reduction of Salmonella on chicken meat and chicken skin by combined or sequential application of lytic bacteriophage with chemical antimicrobials. International Journal of Food Microbiology 207:8–15. doi: 10.1016/j.ijfoodmicro.2015.04.025.
   PubMed Web of Science ®Google Scholar
• Sukumaran, A. T., R. Nannapaneni, A. Kiess, and C. S. Sharma. 2016. Reduction of Salmonella on chicken breast fillets stored under aerobic or modified atmosphere packaging by the application of lytic bacteriophage preparation SalmoFreshTM. Poultry Science 95 (3):668–75. doi: 10.3382/ps/pev332.
   PubMed Web of Science ®Google Scholar
• Sulakvelidze, A., Z. Alavidze, and J. G. Morris, Jr. 2001. Bacteriophage therapy. Antimicrobial Agents and Chemotherapy 45 (3):649–59. doi: 10.1128/AAC.45.3.649-659.2001.
   PubMed Web of Science ®Google Scholar
• Sumrall, E. T., Y. Shen, A. P. Keller, J. Rismondo, M. Pavlou, M. R. Eugster, S. Boulos, O. Disson, P. Thouvenot, S. Kilcher, et al. 2019. Phage resistance at the cost of virulence: Listeria monocytogenes serovar 4b requires galactosylated teichoic acids for InlB-mediated invasion. PLoS Pathogens 15 (10):e1008032. doi: 10.1371/journal.ppat.1008032.
   PubMed Web of Science ®Google Scholar
• Swift, S. M., B. S. Seal, J. K. Garrish, B. B. Oakley, K. Hiett, H. Y. Yeh, R. Woolsey, K. M. Schegg, J. E. Line, and D. M. Donovan. 2015. A thermophilic phage endolysin fusion to a Clostridium perfringens-specific cell wall binding domain creates an anti-Clostridium antimicrobial with improved thermostability. Viruses 7 (6):3019–34. doi: 10.3390/v7062758.
   PubMed Web of Science ®Google Scholar
• Tagliaferri, T. L., M. Jansen, and H.-P. Horz. 2019. Fighting pathogenic bacteria on two fronts: Phages and antibiotics as combined strategy. Frontiers in Cellular and Infection Microbiology 9:22. doi: 10.3389/fcimb.2019.00022.
   PubMed Web of Science ®Google Scholar
• Tamma, P. D., S. E. Cosgrove, and L. L. Maragakis. 2012. Combination therapy for treatment of infections with gram-negative bacteria. Clinical Microbiology Reviews 25 (3):450–70. doi: 10.1128/CMR.05041-11.
   PubMed Web of Science ®Google Scholar
• Tao, P., J. Zhu, M. Mahalingam, H. Batra, and V. B. Rao. 2019. Bacteriophage T4 nanoparticles for vaccine delivery against infectious diseases. Advanced Drug Delivery Reviews 145:57–72. doi: 10.1016/j.addr.2018.06.025.
   PubMed Web of Science ®Google Scholar
• Thomas, M. K., R. Vriezen, J. M. Farber, A. Currie, W. Schlech, and A. Fazil. 2015. Economic cost of a Listeria monocytogenes outbreak in Canada, 2008. Foodborne Pathogens and Disease 12 (12):966–71. doi: 10.1089/fpd.2015.1965.
   PubMed Web of Science ®Google Scholar
• Tom, E. F., I. J. Molineux, M. L. Paff, and J. J. Bull. 2018. Experimental evolution of UV resistance in a phage. PeerJ 6:e5190. doi: 10.7717/peerj.5190.
   PubMed Web of Science ®Google Scholar
• Toro, H., S. B. Price, A. S. McKee, F. J. Hoerr, J. Krehling, M. Perdue, and L. Bauermeister. 2005. Use of bacteriophages in combination with competitive exclusion to reduce Salmonella from infected chickens. Avian Diseases 49 (1):118–24. doi: 10.1637/7286-100404R.
   PubMed Web of Science ®Google Scholar
• Torres-Acosta, M., A. González-Mora, F. Ruiz-Ruiz, M. Rito-Palomares, and J. Benavides. 2020. Economic evaluation of M13 bacteriophage production at large-scale for therapeutic applications using aqueous two-phase systems. Journal of Chemical Technology & Biotechnology 95 (11):2822–33. doi: 10.1002/jctb.6526.
   Web of Science ®Google Scholar
• Torres-Acosta, M. A., V. Clavijo, C. Vaglio, A. F. González-Barrios, M. J. Vives-Flórez, and M. Rito-Palomares. 2019. Economic evaluation of the development of a phage therapy product for the control of Salmonella in poultry. Biotechnology Progress 35 (5):14. doi: 10.1002/btpr.2852.
   Web of Science ®Google Scholar
• Upadhaya, S. D., J. M. Ahn, J. H. Cho, H. B. Kim, J. Y. Kim, D. K. Kang, S. W. Kim, and K. Inho. 2020. Bacteriophage cocktail supplementation improves growth performance, gut microbiome and production traits in broiler chickens. Journal of Animal Science and Biotechnology. doi: 10.21203/rs.3.rs-86723/v1.
   Web of Science ®Google Scholar
• Valério, N., C. Oliveira, V. Jesus, T. Branco, C. Pereira, C. Moreirinha, and A. Almeida. 2017. Effects of single and combined use of bacteriophages and antibiotics to inactivate Escherichia coli. Virus Research 240:8–17. doi: 10.1016/j.virusres.2017.07.015.
   PubMed Web of Science ®Google Scholar
• van Alphen, L. B., C. Q. Wenzel, M. R. Richards, C. Fodor, R. A. Ashmus, M. Stahl, A. V. Karlyshev, B. W. Wren, A. Stintzi, W. G. Miller, et al. 2014. Biological roles of the O-methyl phosphoramidate capsule modification in Campylobacter jejuni. PLoS One 9 (1):e87051. doi: 10.1371/journal.pone.0087051.
   PubMed Web of Science ®Google Scholar
• van Nassau, T. J., C. A. Lenz, A. S. Scherzinger, and R. F. Vogel. 2017. Combination of endolysins and high pressure to inactivate Listeria monocytogenes. Food Microbiology 68:81–8. doi: 10.1016/j.fm.2017.06.005.
   PubMed Web of Science ®Google Scholar
• Vinay, M., N. Franche, G. Gregori, J. R. Fantino, F. Pouillot, and M. Ansaldi. 2015. Phage-based fluorescent biosensor prototypes to specifically detect enteric bacteria such as E. coli and Salmonella enterica Typhimurium. PLoS One 10 (7):e0131466. doi: 10.1371/journal.pone.0131466.
   PubMed Web of Science ®Google Scholar
• Wagenaar, J. A., M. A. Van Bergen, M. A. Mueller, T. M. Wassenaar, and R. M. Carlton. 2005. Phage therapy reduces Campylobacter jejuni colonization in broilers. Veterinary Microbiology 109 (3–4):275–83. doi: 10.1016/j.vetmic.2005.06.002.
   PubMed Web of Science ®Google Scholar
• Wahl, A., A. Battesti, and M. Ansaldi. 2019. Prophages in Salmonella enterica: A driving force in reshaping the genome and physiology of their bacterial host? Molecular Microbiology 111 (2):303–16. doi: 10.1111/mmi.14167.
   PubMed Web of Science ®Google Scholar
• Wang, H., S. Ding, Y. Dong, K. Ye, X. Xu, and G. Zhou. 2013. Biofilm formation of Salmonella serotypes in simulated meat processing environments and its relationship to cell characteristics. Journal of Food Protection 76 (10):1784–9. doi: 10.4315/0362-028X.JFP-13-093.
   PubMed Web of Science ®Google Scholar
• Wang, J. P., L. Yan, J. H. Lee, and I. H. Kim. 2013. Evaluation of bacteriophage supplementation on growth performance, blood characteristics, relative organ weight, breast muscle characteristics and excreta microbial shedding in broilers. Asian-Australasian Journal of Animal Sciences 26 (4):573–8. doi: 10.5713/ajas.2012.12544.
   PubMed Web of Science ®Google Scholar
• Wernicki, A., A. Nowaczek, and R. Urban-Chmiel. 2017. Bacteriophage therapy to combat bacterial infections in poultry. Virology Journal 14 (1):179. doi: 10.1186/s12985-017-0849-7.
   PubMedGoogle Scholar
• Whichard, J. M., N. Sriranganathan, and F. W. Pierson. 2003. Suppression of Salmonella growth by wild-type and large-plaque variants of bacteriophage Felix O1 in liquid culture and on chicken frankfurters. Journal of Food Protection 66 (2):220–5. doi: 10.4315/0362-028X-66.2.220.
   PubMed Web of Science ®Google Scholar
• Wilson, D. J., E. Gabriel, A. J. H. Leatherbarrow, J. Cheesbrough, S. Gee, E. Bolton, A. Fox, P. Fearnhead, C. A. Hart, and P. J. Diggle. 2008. Tracing the source of campylobacteriosis. PLoS Genetics 4 (9):e1000203. doi: 10.1371/journal.pgen.1000203.
   PubMed Web of Science ®Google Scholar
• Wójcik, E. A., A. Wojtasik, E. Górecka, and M. Stańczyk. 2014. Application of bacteriophage preparation Bafasal in broiler chickens experimentally exposed to Salmonella spp.
   Google Scholar
• Wong, C. L., C. C. Sieo, W. S. Tan, N. Abdullah, M. Hair-Bejo, J. Abu, and Y. W. Ho. 2014. Evaluation of a lytic bacteriophage, Φ st1, for biocontrol of Salmonella enterica serovar Typhimurium in chickens. International Journal of Food Microbiology 172:92–101. doi: 10.1016/j.ijfoodmicro.2013.11.034.
   PubMed Web of Science ®Google Scholar
• Wright, R. C. T., V.-P. Friman, M. C. M. Smith, and M. A. Brockhurst. 2019. Resistance evolution against phage combinations depends on the timing and order of exposure. mBio 10 (5):e01652-19. doi: 10.1128/mBio.01652-19.
   PubMed Web of Science ®Google Scholar
• Yang, S., M. Sadekuzzaman, and S. D. Ha. 2017. Reduction of Listeria monocytogenes on chicken breasts by combined treatment with UV-C light and bacteriophage ListShield. LWT - Food Science and Technology 86 (1):193–200. doi: 10.1016/j.lwt.2017.07.060.
   Google Scholar
• Yang, Z., S. Yin, G. Li, J. Wang, G. Huang, B. Jiang, B. You, Y. Gong, C. Zhang, X. Luo, et al. 2019. Global transcriptomic analysis of the interactions between phage φAbp1 and extensively drug-resistant Acinetobacter baumannii. mSystems 4 (2):e00068-19. doi: 10.1128/mSystems.00068-19.
   PubMed Web of Science ®Google Scholar
• Yehl, K., S. Lemire, A. C. Yang, H. Ando, M. Mimee, M. D. T. Torres, C. de la Fuente-Nunez, and T. K. Lu. 2019. Engineering phage host-range and suppressing bacterial resistance through phage tail fiber mutagenesis. Cell 179 (2):459–69.e9. doi: 10.1016/j.cell.2019.09.015.
   PubMed Web of Science ®Google Scholar
• Yin, J., Z. Cheng, X. Wang, L. Xu, Q. Li, S. Geng, and X. Jiao. 2015. Evaluation of the Salmonella enterica serovar Pullorum pathogenicity island 2 mutant as a candidate live attenuated oral vaccine. Clinical and Vaccine Immunology: CVI 22 (7):706–10. doi: 10.1128/cvi.00130-15.
   PubMedGoogle Scholar
• Yuan, Y., and M. Gao. 2016. Proteomic analysis of a novel Bacillus Jumbo phage revealing glycoside hydrolase as structural component. Frontiers in Microbiology 7:745. doi: 10.3389/fmicb.2016.00745.
   PubMed Web of Science ®Google Scholar
• Żbikowska, K., M. Michalczuk, and B. Dolka. 2020. The use of bacteriophages in the poultry industry. Animals 10 (5):872. doi: 10.3390/ani10050872.
   Web of Science ®Google Scholar
• Zhang, H., H. Bao, C. Billington, J. A. Hudson, and R. Wang. 2012. Isolation and lytic activity of the Listeria bacteriophage endolysin LysZ5 against Listeria monocytogenes in soya milk. Food Microbiology 31 (1):133–6. doi: 10.1016/j.fm.2012.01.005.
   PubMed Web of Science ®Google Scholar
• Zhao, P. Y., H. Y. Baek, and I. H. Kim. 2012. Effects of bacterio­phage supplementation on egg performance, egg quality, excreta ­microflora, and moisture content in laying hens. Asian-Australasian Journal of Animal Sciences 25 (7):1015–20. doi: 10.5713/ajas.2012.12026.
   PubMed Web of Science ®Google Scholar
• Zhao, X., C. Chen, W. Shen, G. Huang, S. Le, S. Lu, M. Li, Y. Zhao, J. Wang, X. Rao, et al. 2016. Global transcriptomic analysis of interactions between Pseudomonas aeruginosa and bacteriophage PaP3. Scientific Reports 6 (1):19237. doi: 10.1038/srep19237.
   PubMedGoogle Scholar
• Zhao, X., M. Shen, X. Jiang, W. Shen, Q. Zhong, Y. Yang, Y. Tan, M. Agnello, X. He, F. Hu, et al. 2017. Transcriptomic and metabolomics profiling of phage-host interactions between phage PaP1 and Pseudomonas aeruginosa. Frontiers in Microbiology 8:548. doi: 10.3389/fmicb.2017.00548.
   PubMedGoogle Scholar
• Zimmer, M., S. Scherer, and M. J. Loessner. 2002. Genomic analysis of Clostridium perfringens bacteriophage phi3626, which integrates into guaA and possibly affects sporulation. Journal of Bacteriology 184 (16):4359–68. doi: 10.1128/jb.184.16.4359-4368.2002.
   PubMed Web of Science ®Google Scholar
• Zinno, P., C. Devirgiliis, D. Ercolini, D. Ongeng, and G. Mauriello. 2014. Bacteriophage P22 to challenge Salmonella in foods. International Journal of Food Microbiology 191:69–74. doi: 10.1016/j.ijfoodmicro.2014.08.037.
   PubMed Web of Science ®Google Scholar