Tack DM, Ray L, Griffin PM, Cieslak PR, Dunn J, Rissman T, et al. Preliminary incidence and trends of infections with pathogens transmitted commonly through food — foodborne diseases active surveillance network, 10 U.S. sites, 2016–2019. MMWR Morb Mortal Wkly Rep. 2020;69:509–14. https://doi.org/10.15585/mmwr.mm6917a1.
CDC. Salmonella. https://www.cdc.gov/salmonella/index.html#:~:text=CDC%20estimates%20Salmonella%20bacteria%20cause,%2C%20fever%2C%20and%20stomach%20cramps. [Accessed 27 September 2024].
Barrow PA, Jones MA, Smith AL, Wigley P. The long view: Salmonella – the last forty years. Avian Pathol. 2012;41:413–20. https://doi.org/10.1080/03079457.2012.718071.
Cosby DE, Cox NA, Harrison MA, Wilson JL, Buhr RJ, Fedorka-Cray PJ. Salmonella and antimicrobial resistance in broilers: a review. J Appl Poult Res. 2015;24:408–26. https://doi.org/10.3382/japr/pfv038.
McMillan EA, Weinroth MD, Frye JG. Increased prevalence of Salmonella infantis isolated from raw chicken and Turkey products in the United States is due to a single clonal lineage carrying the pESI plasmid. Microorganisms. 2022;10:1478. https://doi.org/10.3390/microorganisms10071478.
Montoro-Dasi L, Lorenzo-Rebenaque L, Marco-Fuertes A, Vega S, Marin C. Holistic strategies to control Salmonella infantis: an emerging challenge in the European broiler sector. Microorganisms. 2023;11:1765. https://doi.org/10.3390/microorganisms11071765.
Piña-Iturbe A, Díaz-Gavidia C, Álvarez FP, Barron-Montenegro R, Álvarez-Espejo DM, García P, et al. Genomic characterisation of the population structure and antibiotic resistance of Salmonella enterica serovar infantis in Chile, 2009–2022. The Lancet Regional Health. 2024;32:100711. https://doi.org/10.1016/j.lana.2024.100711.
Mejía L, Medina JL, Bayas R, Salazar CS, Villavicencio F, Zapata S, et al. Genomic epidemiology of Salmonella infantis in Ecuador: from poultry farms to human infections. Front Vet Sci. 2020;7:547891. https://doi.org/10.3389/fvets.2020.547891.
Mattock J, Chattaway MA, Hartman H, Dallman TJ, Smith AM, Keddy K, et al. A one health perspective on Salmonella enterica serovar Infantis, an emerging human multidrug-resistant pathogen. Emerg Infect Dis. 2024;30:701–10. https://doi.org/10.3201/eid3004.231031.
Sevilla-Navarro S, Torres-Boncompte J, Garcia-Llorens J, Bernabéu-Gimeno M, Domingo-Calap P, Catalá-Gregori P. Fighting Salmonella infantis: bacteriophage-driven cleaning and disinfection strategies for broiler farms. Front Microbiol. 2024;15:1401479. https://doi.org/10.3389/fmicb.2024.1401479.
Kahn LH, Bergeron G, Bourassa MW, De Vegt B, Gill J, Gomes F, et al. From farm management to bacteriophage therapy: strategies to reduce antibiotic use in animal agriculture. Ann N Y Acad Sci. 2019;1441:31–9. https://doi.org/10.1111/nyas.14034.
O’Sullivan L, Bolton D, McAuliffe O, Coffey A. Bacteriophages in food applications: from foe to friend. Annu Rev Food Sci Technol. 2019;10:151–72. https://doi.org/10.1146/annurev-food-032818-121747.
Nobrega FL, Vlot M, de Jonge PA, Dreesens LL, Beaumont HJE, Lavigne R, et al. Targeting mechanisms of tailed bacteriophages. Nat Rev Microbiol. 2018;16:760–73. https://doi.org/10.1038/s41579-018-0070-8.
Clokie MR, Millard AD, Letarov AV, Heaphy S. Phages in nature. Bacteriophage. 2011;1:31–45. https://doi.org/10.4161/bact.1.1.14942.
Pelyuntha W, Ngasaman R, Yingkajorn M, Chukiatsiri K, Benjakul S, Vongkamjan K. Isolation and characterization of potential Salmonella phages targeting Multidrug-Resistant and major serovars of Salmonella derived from broiler production chain in Thailand. Front Microbiol. 2021;12:662461. https://doi.org/10.3389/fmicb.2021.662461.
Panec M, Katz DS. Plaque assay protocols. In Protocols. American Society for Microbiology, Washington, DC. https://asm.org/protocols/plaque-assay-protocols. Accessed 20 Sept 2025.
Lennon M, Liao Y-T, Salvador A, Lauzon CR, Wu VCH. Bacteriophages specific to Shiga toxin-producing Escherichia coli exist in goat feces and associated environments on an organic produce farm in Northern California, USA. PLoS ONE. 2020;15:e0234438. https://doi.org/10.1371/journal.pone.0234438.
Zhang Y, Liao Y-T, Salvador A, Lavenburg VM, Wu VCH. Characterization of two new Shiga toxin-producing Escherichia coli O103-infecting phages isolated from an organic farm. Microorganisms. 2021;9:1527. https://doi.org/10.3390/microorganisms9071527.
Wick RR, Judd LM, Gorrie CL, Holt KE, Unicycler. Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13:e1005595. https://doi.org/10.1371/journal.pcbi.1005595.
Garneau JR, Depardieu F, Fortier L-C, Bikard D, Monot M. PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data. Sci Rep. 2017;7:8292. https://doi.org/10.1038/s41598-017-07910-5.
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9. https://doi.org/10.1093/bioinformatics/btu153.
UniProt Consortium. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 2021;49:D480–9. https://doi.org/10.1093/nar/gkaa1100.
Lowe TM, Chan PP. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 2016;44:W54–57. https://doi.org/10.1093/nar/gkw413.
Malberg Tetzschner AM, Johnson JR, Johnston BD, Lund O, Scheutz F. In Silico genotyping of Escherichia coli isolates for extraintestinal virulence genes by use of Whole-Genome sequencing data. J Clin Microbiol. 2020;58:e01269–20. https://doi.org/10.1128/JCM.01269-20.
Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother. 2020;75:3491–500. https://doi.org/10.1093/jac/dkaa345.
Zhang Y, Mao M, Zhang R, Liao Y-T, Wu VCH. Deeppl: a deep-learning-based tool for the prediction of bacteriophage lifecycle. PLoS Comput Biol. 2024;20:e1012525. https://doi.org/10.1371/journal.pcbi.1012525.
Meier-Kolthoff JP, Göker M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics. 2017;33:3396–404. https://doi.org/10.1093/bioinformatics/btx440.
Mahadevan P, King JF, Seto D, CGUG. Silico proteome and genome parsing tool for the determination of core and unique genes in the analysis of genomes up to ca. 1.9 Mb. BMC Res Notes. 2009;2:168. https://doi.org/10.1186/1756-0500-2-168.
Liao Y-T, Zhang Y, Salvador A, Ho K-J, Cooley MB, Wu VCH. Characterization of polyvalent Escherichia phage Sa157lw for the biocontrol potential of Salmonella Typhimurium and Escherichia coli O157:H7 on contaminated mung bean seeds. Front Microbiol. 2022;13:1053583. https://doi.org/10.3389/fmicb.2022.1053583.
Acton L, Pye HV, Thilliez G, Kolenda R, Matthews M, Turner AK, et al. Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica. J Virol. 2024;98:e01476–23. https://doi.org/10.1128/jvi.01476-23.
Skutel M, Andriianov A, Zavialova M, Kirsanova M, Shodunke O, Zorin E, et al. T5-like phage BF23 evades host-mediated DNA restriction and methylation. MicroLife. 2023;4:uqad044. https://doi.org/10.1093/femsml/uqad044.
Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992;8:275–82. https://doi.org/10.1093/bioinformatics/8.3.275.
Liao Y-T, Salvador A, Harden LA, Liu F, Lavenburg VM, Li RW, et al. Characterization of a lytic bacteriophage as an antimicrobial agent for biocontrol of Shiga Toxin-Producing Escherichia coli O145 strains. Antibiotics. 2019;8:74. https://doi.org/10.3390/antibiotics8020074.
Liao Y-T, Ho K-J, Zhang Y, Salvador A, Wu VCH. A new rogue-like Escherichia phage UDF157lw to control Escherichia coli O157:H7. Front Microbiol. 2024;14:1302032. https://doi.org/10.3389/fmicb.2023.1302032.
Liao Y-T, Zhang Y, Salvador A, Harden LA, Wu VCH. Characterization of a T4-like bacteriophage vB_EcoM-Sa45lw as a potential biocontrol agent for Shiga Toxin-Producing Escherichia coli O45 contaminated on mung bean seeds. Microbiol Spectr. 2022;10:e0222021. https://doi.org/10.1128/spectrum.02220-21.
Wu VCH. A review of microbial injury and recovery methods in food. Food Microbiol. 2008;25:735–44. https://doi.org/10.1016/j.fm.2008.04.011.
Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics. 2016;32:929–31. https://doi.org/10.1093/bioinformatics/btv681.
Turner D, Kropinski AM, Adriaenssens EM. A roadmap for genome-based phage taxonomy. Viruses. 2021;13:506. https://doi.org/10.3390/v13030506.
Wang J, Jiang Y, Vincent M, Sun Y, Yu H, Wang J, et al. Complete genome sequence of bacteriophage T5. Virology. 2005;332:45–65. https://doi.org/10.1016/j.virol.2004.10.049.
Drauch V, Ibesich C, Vogl C, Hess M, Hess C. In-vitro testing of bacteriostatic and bactericidal efficacy of commercial disinfectants against Salmonella infantis reveals substantial differences between products and bacterial strains. Int J Food Microbiol. 2020;328:108660. https://doi.org/10.1016/j.ijfoodmicro.2020.108660.
Moraes JO, Cruz EA, Souza EGF, Oliveira TCM, Alvarenga VO, Peña WEL, et al. Predicting adhesion and biofilm formation boundaries on stainless steel surfaces by five Salmonella enterica strains belonging to different serovars as a function of pH, temperature and NaCl concentration. Int J Food Microbiol. 2018;281:90–100. https://doi.org/10.1016/j.ijfoodmicro.2018.05.011.
Moye ZD, Das CR, Tokman JI, Fanelli B, Karathia H, Hasan NA, et al. Treatment of fresh produce with a Salmonella-targeted bacteriophage cocktail is compatible with chlorine or peracetic acid and more consistently preserves the microbial community on produce. J Food Saf. 2020;40:e12763. https://doi.org/10.1111/jfs.12763.
Pinto G, Almeida C, Azeredo J. Bacteriophages to control Shiga toxin-producing E. coli – safety and regulatory challenges. Crit Rev Biotechnol. 2020;40:1081–97. https://doi.org/10.1080/07388551.2020.1805719.
Vikram A, Tokman JI, Woolston J, Sulakvelidze A. Phage biocontrol improves food safety by significantly reducing the level and prevalence of Escherichia coli O157:H7 in various foods. J Food Prot. 2020;83:668–76. https://doi.org/10.4315/0362-028X.JFP-19-433.
Mojica-a T, Garcia E. Growth of coliphage BF23 on rough strains of Salmonella typhimurium: the Bfe locus. Mol Gen Genet. 1976;147:195–202. https://doi.org/10.1007/BF00267571.
Degroux S, Effantin G, Linares R, Schoehn G, Breyton C. Deciphering bacteriophage T5 host recognition mechanism and infection trigger. J Virol. 2023;97:e01584–22. https://doi.org/10.1128/jvi.01584-22.
Lathrop JT, Wei BY, Touchie GA, Kadner RJ. Sequences of the Escherichia coli BtuB protein essential for its insertion and function in the outer membrane. J Bacteriol. 1995;177:6810–9. https://doi.org/10.1128/jb.177.23.6810-6819.1995.
Golomidova AK, Kulikov EE, Prokhorov NS, Guerrero-Ferreira RС, Knirel YA, Kostryukova ES, et al. Branched lateral tail fiber organization in T5-like bacteriophages DT57C and DT571/2 is revealed by genetic and functional analysis. Viruses. 2016;8:26. https://doi.org/10.3390/v8010026.
Pyra A, Filik K, Szermer-Olearnik B, Czarny A, Brzozowska E. New insights on the feature and function of tail tubular protein B and tail fiber protein of the lytic bacteriophage φYeO3-12 specific for Yersinia enterocolitica serotype O:3. Molecules. 2020;25:4392. https://doi.org/10.3390/molecules25194392.
Steven AC, Trus BL, Maizel JV, Unser M, Parry DA, Wall JS, et al. Molecular substructure of a viral receptor-recognition protein. The gp17 tail-fiber of bacteriophage T7. J Mol Biol. 1988;200:351–65. https://doi.org/10.1016/0022-2836(88)90246-x.
Gehl B, Sweetlove LJ. Mitochondrial band-7 family proteins: scaffolds for respiratory chain assembly. Front Plant Sci. 2014;5:141. https://doi.org/10.3389/fpls.2014.00141.
Zhang Y, Chu M, Liao Y-T, Salvador A, Wu VCH. Characterization of two novel Salmonella phages having biocontrol potential against Salmonella spp. in gastrointestinal conditions. Sci Rep. 2024;14:12294. https://doi.org/10.1038/s41598-024-59502-9.
Guo Y, Li J, Islam MS, Yan T, Zhou Y, Liang L, et al. Application of a novel phage vB_SalS-LPSTLL for the biological control of Salmonella in foods. Food Res Int. 2021;147:110492. https://doi.org/10.1016/j.foodres.2021.110492.
Nilsson AS. Phage therapy–constraints and possibilities. Ups J Med Sci. 2014;119:192–8. https://doi.org/10.3109/03009734.2014.902878.
Duc HM, Son HM, Yi HPS, Sato J, Ngan PH, Masuda Y, et al. Isolation, characterization and application of a polyvalent phage capable of controlling Salmonella and Escherichia coli O157:H7 in different food matrices. Food Res Int. 2020;131:108977. https://doi.org/10.1016/j.foodres.2020.108977.
Malik DJ. Approaches for manufacture, formulation, targeted delivery and controlled release of phage-based therapeutics. Curr Opin Biotechnol. 2021;68:262–71. https://doi.org/10.1016/j.copbio.2021.02.009.
Islam MS, Zhou Y, Liang L, Nime I, Liu K, Yan T, et al. Application of a phage cocktail for control of Salmonella in foods and reducing biofilms. Viruses. 2019;11:841. https://doi.org/10.3390/v11090841.
Abedon ST. Lysis from without. Bacteriophage. 2011;1:46–9. https://doi.org/10.4161/bact.1.1.13980.
Erol HB, Kaskatepe B. Effect of phage and rhamnolipid on Salmonella Infantis biofilm removal and biological control of phage on food deterioration. Int J Food Sci Tech. 2024;59:120–8. https://doi.org/10.1111/ijfs.16781.
Wandro S, Ghatbale P, Attai H, Hendrickson C, Samillano C, Suh J, et al. Phage Cocktails Constrain the Growth of Enterococcus. mSystems. 2022;7:e0001922. https://doi.org/10.1128/msystems.00019-22.
Martinez-Soto CE, McClelland M, Kropinski AM, Lin JT, Khursigara CM, Anany H. Multireceptor phage cocktail against Salmonella enterica to circumvent phage resistance. Microlife. 2024;5:uqae003. https://doi.org/10.1093/femsml/uqae003.
Fong K, Mu K, Rheault J-G, Levesque RC, Kitts DD, Delaquis P, et al. Bacteriophage-insensitive mutants of antimicrobial-resistant Salmonella Enterica are altered in their tetracycline resistance and virulence in Caco-2 intestinal cells. Int J Mol Sci. 2020;21:1883. https://doi.org/10.3390/ijms21051883.
McGee LW, Barhoush Y, Shima R, Hennessy M. Phage-resistant mutations impact bacteria susceptibility to future phage infections and antibiotic response. Ecol Evol. 2023;13:e9712. https://doi.org/10.1002/ece3.9712.