{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T12:46:23Z","timestamp":1791809183883,"version":"4.3.4"},"reference-count":93,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T00:00:00Z","timestamp":1783728000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T00:00:00Z","timestamp":1791763200000},"content-version":"vor","delay-in-days":93,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"VRI Doctoral Fellowship"},{"name":"ANID National Doctoral Fellowship","award":["N\u00b0 21251772"],"award-info":[{"award-number":["N\u00b0 21251772"]}]},{"DOI":"10.13039\/501100002850","name":"Fondo Nacional de Desarrollo Cient\u00edfico y Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["N\u00b0 1240971"],"award-info":[{"award-number":["N\u00b0 1240971"]}],"id":[{"id":"10.13039\/501100002850","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002850","name":"Fondo Nacional de Desarrollo Cient\u00edfico y Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["N\u00b0 1231851"],"award-info":[{"award-number":["N\u00b0 1231851"]}],"id":[{"id":"10.13039\/501100002850","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002850","name":"Fondo Nacional de Desarrollo Cient\u00edfico y Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["N\u00b0 1231905"],"award-info":[{"award-number":["N\u00b0 1231905"]}],"id":[{"id":"10.13039\/501100002850","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Millennium Institute of Immunology and Immunotherapy","award":["ICN 2021_045"],"award-info":[{"award-number":["ICN 2021_045"]}]},{"name":"ECOS-ANID","award":["ECOS220027"],"award-info":[{"award-number":["ECOS220027"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"DOI":"10.1186\/s12866-026-05329-5","type":"journal-article","created":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T06:14:45Z","timestamp":1783750485000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Whole genome sequence-based comparative genomics reveals preliminary genomic features of Salmonella enterica subsp. enterica serovar Enteritidis phage type 1 and phage type 4 strains from EnteroBase"],"prefix":"10.1186","volume":"26","author":[{"given":"Lucas","family":"V\u00e1squez-Herrera","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Omar P.","family":"Vallejos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9","family":"Acevedo-L\u00f3pez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sof\u00eda","family":"Campos-Gajardo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"Pi\u00f1a-Iturbe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Tichy-Navarro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dwayne","family":"Seeram","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne-Catrin","family":"Uhlemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pablo A.","family":"Gonz\u00e1lez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexis M.","family":"Kalergis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea I.","family":"Moreno-Switt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan M.","family":"Bueno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,11]]},"reference":[{"key":"5329_CR1","doi-asserted-by":"publisher","first-page":"1593219","DOI":"10.3389\/fcimb.2025.1593219","volume":"15","author":"E Gomes","year":"2025","unstructured":"Gomes E, Ara\u00fajo D, Nogueira T, Oliveira R, Silva S, Oliveira LVN, et al. Advances in whole genome sequencing for foodborne pathogens: implications for clinical infectious disease surveillance and public health. Front Cell Infect Microbiol. 2025;15:1593219. https:\/\/doi.org\/10.3389\/fcimb.2025.1593219.","journal-title":"Front Cell Infect Microbiol"},{"issue":"2","key":"5329_CR2","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1017\/s0950268800067765","volume":"99","author":"LR Ward","year":"1987","unstructured":"Ward LR, de Sa JD, Rowe B. A phage-typing scheme for Salmonella enteritidis. Epidemiol Infect. 1987;99(2):291\u20134. https:\/\/doi.org\/10.1017\/s0950268800067765.","journal-title":"Epidemiol Infect"},{"key":"5329_CR3","doi-asserted-by":"publisher","unstructured":"Rabsch W. (2007). Salmonella Typhimurium phage typing for pathogens. In H. Schatten & A. Eisenstark (Eds.), Salmonella (Vol. 394, pp. 177\u2013211). Humana Press. https:\/\/doi.org\/10.1007\/978-1-59745-512-1_10","DOI":"10.1007\/978-1-59745-512-1_10"},{"issue":"2","key":"5329_CR4","doi-asserted-by":"publisher","first-page":"105","DOI":"10.4161\/bact.19274","volume":"2","author":"DA Schofield","year":"2012","unstructured":"Schofield DA, Sharp NJ, Westwater C. Phage-based platforms for the clinical detection of human bacterial pathogens. Bacteriophage. 2012;2(2):105\u2013283. https:\/\/doi.org\/10.4161\/bact.19274.","journal-title":"Bacteriophage"},{"issue":"2","key":"5329_CR5","doi-asserted-by":"publisher","first-page":"223","DOI":"10.3390\/pathogens12020223","volume":"12","author":"MA Chattaway","year":"2023","unstructured":"Chattaway MA, Painset A, Godbole G, Gharbia S, Jenkins C. Evaluation of genomic typing methods in the Salmonella reference laboratory in public health, England, 2012\u20132020. Pathogens (Basel, Switzerland). 2023;12(2):223. https:\/\/doi.org\/10.3390\/pathogens12020223.","journal-title":"Pathogens (Basel, Switzerland)"},{"issue":"1","key":"5329_CR6","doi-asserted-by":"publisher","first-page":"76","DOI":"10.18502\/ijm.v14i1.8806","volume":"14","author":"MR Arabestani","year":"2022","unstructured":"Arabestani MR, Kamarehei F, Dini M, Aziz Jalilian F, Moradi A, Shokoohizadeh L. Characterization of\u00a0Staphylococcus aureus\u00a0isolates from pastry samples by rep-PCR and phage typing. Iran J Microbiol. 2022;14(1):76\u201383. https:\/\/doi.org\/10.18502\/ijm.v14i1.8806.","journal-title":"Iran J Microbiol"},{"issue":"1","key":"5329_CR7","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1186\/s13104-019-4627-z","volume":"12","author":"Z Hashemizadeh","year":"2019","unstructured":"Hashemizadeh Z, Hadi N, Mohebi S, Kalantar-Neyestanaki D, Bazargani A. Characterization of SCCmec, spa types and multi drug resistant of methicillin-resistant staphylococcus aureus isolates among inpatients and outpatients in a referral hospital in Shiraz Iran. BMC Res Notes. 2019;12(1):614. https:\/\/doi.org\/10.1186\/s13104-019-4627-z.","journal-title":"BMC Res Notes"},{"key":"5329_CR8","doi-asserted-by":"publisher","first-page":"104135","DOI":"10.1016\/j.fm.2022.104135","volume":"109","author":"Y Hong","year":"2023","unstructured":"Hong Y, Ji R, Wang Z, Gu J, Jiao X, Li Q. Development and application of a multiplex PCR method to differentiate Salmonella enterica serovar Typhimurium from its monophasic variants in pig farms. Food Microbiol. 2023;109:104135. https:\/\/doi.org\/10.1016\/j.fm.2022.104135.","journal-title":"Food Microbiol"},{"key":"5329_CR9","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1016\/j.ijfoodmicro.2023.110151","volume":"11051","author":"L Sielski Galv\u00e3o Soares","year":"2023","unstructured":"Sielski Galv\u00e3o Soares L, Casella T, Kawagoe EK, Benetti Filho V, Omori WP, Nogueira MCL, et al. Phenotypic and genotypic characterization of antibiotic resistance of Salmonella Heidelberg in the south of Brazil. Intern J Food Microbiol. 2023;11051:391\u20133. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2023.110151.","journal-title":"Intern J Food Microbiol"},{"issue":"1","key":"5329_CR10","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1186\/s13099-025-00679-3","volume":"17","author":"S Vakili","year":"2025","unstructured":"Vakili S, Haeili M, Feizi A, Moghaddasi K, Omrani M, Ghodousi A, et al. Whole-genome sequencing-based characterization of Salmonella enterica Serovar Enteritidis and Kentucky isolated from laying hens in northwest of Iran, 2022\u20132023. Gut pathogens. 2025;17(1):2. https:\/\/doi.org\/10.1186\/s13099-025-00679-3.","journal-title":"Gut pathogens"},{"issue":"1","key":"5329_CR11","doi-asserted-by":"publisher","first-page":"76","DOI":"10.3390\/antibiotics13010076","volume":"13","author":"B Lamichhane","year":"2024","unstructured":"Lamichhane B, Mawad AMM, Saleh M, Kelley WG, Harrington PJ 2nd, Lovestad CW, et al. Salmonellosis: an overview of epidemiology, pathogenesis, and innovative approaches to mitigate the antimicrobial resistant infections. Antibiotics (Basel, Switzerland). 2024;13(1):76. https:\/\/doi.org\/10.3390\/antibiotics13010076.","journal-title":"Antibiotics (Basel, Switzerland)"},{"key":"5329_CR12","doi-asserted-by":"publisher","first-page":"1524287","DOI":"10.3389\/fmicb.2025.1524287","volume":"16","author":"G Kumar","year":"2025","unstructured":"Kumar G, Kumar S, Jangid H, Dutta J, Shidiki A. The rise of non-typhoidal Salmonella: an emerging global public health concern. Front Microbiol. 2025;16:1524287. https:\/\/doi.org\/10.3389\/fmicb.2025.1524287.","journal-title":"Front Microbiol"},{"issue":"12","key":"5329_CR13","doi-asserted-by":"publisher","first-page":"2817","DOI":"10.1128\/jcm.29.12.2817-2823.1991","volume":"29","author":"FW Hickman-Brenner","year":"1991","unstructured":"Hickman-Brenner FW, Stubbs AD, Farmer JJ 3rd. Phage typing of Salmonella enteritidis in the United States. J Clin Microbiol. 1991;29(12):2817\u201323. https:\/\/doi.org\/10.1128\/jcm.29.12.2817-2823.1991.","journal-title":"J Clin Microbiol"},{"issue":"1","key":"5329_CR14","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1017\/s0950268800056417","volume":"106","author":"R Khakhria","year":"1991","unstructured":"Khakhria R, Duck D, Lior H. Distribution of Salmonella enteritidis phage types in Canada. Epidemiol Infect. 1991;106(1):25\u201332. https:\/\/doi.org\/10.1017\/s0950268800056417.","journal-title":"Epidemiol Infect"},{"issue":"5","key":"5329_CR15","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1007\/BF01719587","volume":"10","author":"A Schroeter","year":"1994","unstructured":"Schroeter A, Ward LR, Rowe B, Protz D, Hartung M, Helmuth R. Salmonella enteritidis phage types in Germany. Eur J Epidemiol. 1994;10(5):645\u20138. https:\/\/doi.org\/10.1007\/BF01719587.","journal-title":"Eur J Epidemiol"},{"issue":"7","key":"5329_CR16","doi-asserted-by":"publisher","first-page":"2176","DOI":"10.1128\/JCM.37.7.2176-2182.1999","volume":"37","author":"S Lukinmaa","year":"1999","unstructured":"Lukinmaa S, Schildt R, Rinttil\u00e4 T, Siitonen A. Salmonella enteritidis phage types 1 and 4: Pheno- and genotypic epidemiology of recent outbreaks in Finland. J Clin Microbiol. 1999;37(7):2176\u201382. https:\/\/doi.org\/10.1128\/JCM.37.7.2176-2182.1999.","journal-title":"J Clin Microbiol"},{"issue":"11","key":"5329_CR17","doi-asserted-by":"publisher","first-page":"3980","DOI":"10.1128\/JCM.40.11.3980-3985.2002","volume":"40","author":"E van Duijkeren","year":"2002","unstructured":"van Duijkeren E, Wannet WJ, Houwers DJ, van Pelt W. Serotype and phage type distribution of salmonella strains isolated from humans, cattle, pigs, and chickens in the Netherlands from 1984 to 2001. J Clin Microbiol. 2002;40(11):3980\u20135. https:\/\/doi.org\/10.1128\/JCM.40.11.3980-3985.2002.","journal-title":"J Clin Microbiol"},{"issue":"5","key":"5329_CR18","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1017\/S0950268805004474","volume":"133","author":"IA Gillespie","year":"2005","unstructured":"Gillespie IA, O\u2019Brien SJ, Adak GK, Ward LR, Smith HR. Foodborne general outbreaks of Salmonella Enteritidis phage type 4 infection, England and Wales, 1992\u20132002: where are the risks? Epidemiol Infect. 2005;133(5):795\u2013801. https:\/\/doi.org\/10.1017\/S0950268805004474.","journal-title":"Epidemiol Infect"},{"key":"5329_CR19","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1016\/j.fm.2017.04.005","volume":"71","author":"S Kanagarajah","year":"2018","unstructured":"Kanagarajah S, Waldram A, Dolan G, Jenkins C, Ashton PM, Carrion Martin AI, et al. Whole genome sequencing reveals an outbreak of Salmonella Enteritidis associated with reptile feeder mice in the United Kingdom, 2012\u20132015. Food Microbiol. 2018;71:32\u20138. https:\/\/doi.org\/10.1016\/j.fm.2017.04.005.","journal-title":"Food Microbiol"},{"issue":"3","key":"5329_CR20","doi-asserted-by":"publisher","first-page":"001677","DOI":"10.1099\/mgen.0.001677","volume":"12","author":"H Strydom","year":"2026","unstructured":"Strydom H, Paine S, Welch D, Wright J, Bromhead C, Niebuhr CN, et al. Phylodynamic analysis of Salmonella Enteritidis ST183 in Aotearoa New Zealand finds no evidence for introduction via European hedgehogs (Erinaceus europaeus). Microbial Genomics. 2026;12(3):001677. https:\/\/doi.org\/10.1099\/mgen.0.001677.","journal-title":"Microbial Genomics"},{"issue":"3","key":"5329_CR21","doi-asserted-by":"publisher","first-page":"567","DOI":"10.2307\/1591810","volume":"39","author":"RK Gast","year":"1995","unstructured":"Gast RK, Benson ST. The comparative virulence for chicks of Salmonella enteritidis phage type 4 isolates and isolates of phage types commonly found in poultry in the United States. Avian Dis. 1995;39(3):567\u201374. https:\/\/doi.org\/10.2307\/1591810.","journal-title":"Avian Dis"},{"key":"5329_CR22","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1111\/j.1472-765X.1991.tb00536.x","volume":"12","author":"H Chart","year":"1991","unstructured":"Chart H, Threlfall EJ, Rowe B. Virulence studies of Salmonella enteritidis phage types. Lett Appl Microbiol. 1991;12:188\u201391. https:\/\/doi.org\/10.1111\/j.1472-765X.1991.tb00536.x.","journal-title":"Lett Appl Microbiol"},{"issue":"1","key":"5329_CR23","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1590\/s1020-49892001000100004","volume":"9","author":"S Prat","year":"2001","unstructured":"Prat S, Fern\u00e1ndez A, Fica A, Fern\u00e1ndez J, Alexandre M, Heitmann I. Tipificaci\u00f3n f\u00e1gica de aislados de Salmonella enteritidis de muestras cl\u00ednicas, alimentarias y av\u00edcolas en Chile [Phage typing of Salmonella enteritidis isolated from clinical, food, and poultry samples in Chile]. Revista Panamericana de Salud Publica Pan Am J Public Health. 2001;9(1):7\u201312. https:\/\/doi.org\/10.1590\/s1020-49892001000100004.","journal-title":"Revista Panamericana de Salud Publica Pan Am J Public Health"},{"issue":"2","key":"5329_CR24","doi-asserted-by":"publisher","first-page":"85","DOI":"10.4067\/S0716-10182001000200002","volume":"18","author":"A Fica","year":"2001","unstructured":"Fica A, Prat S, Fern\u00e1ndez A, Fern\u00e1ndez J, Heitmann I. Cambios epidemiol\u00f3gicos de las salmonelosis en Chile: Desde Salmonella typhi a Salmonella enteritidis. [Changes in Epidemiological patterns of salmonelosis in Chile. Since Salmonella typhi to Salmonella enteritidis] Revista chilena de infectolog\u00eda. Chilean J Infect. 2001;18(2):85\u201393. https:\/\/doi.org\/10.4067\/S0716-10182001000200002.","journal-title":"Chilean J Infect"},{"key":"5329_CR25","unstructured":"Public Health Institute of Chile. (2019). Laboratory surveillance bulletin: Salmonella spp. 2014\u20132018. https:\/\/www.ispch.cl\/sites\/default\/files\/Bolet%C3%ADnSalmonella-12052020A.pdf"},{"key":"5329_CR26","doi-asserted-by":"publisher","first-page":"101179","DOI":"10.1016\/j.lana.2025.101179","volume":"48","author":"A Pi\u00f1a-Iturbe","year":"2025","unstructured":"Pi\u00f1a-Iturbe A, Adell AD, Reyes-Jara A, Toro M, Moreno-Switt AI. Salmonella in Chile: an urgent need for timely data and WGS implementation. Lancet Reg Health Am. 2025;48:101179. https:\/\/doi.org\/10.1016\/j.lana.2025.101179.","journal-title":"Lancet Reg Health Am"},{"issue":"1","key":"5329_CR27","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1099\/jmm.0.000034-0","volume":"58","author":"N De Lappe","year":"2009","unstructured":"De Lappe N, Doran G, O\u2019connor J, O\u2019hare C, Cormican M. Characterization of bacteriophages used in the Salmonella enterica serovar Enteritidis phage-typing scheme. J Med Microbiol. 2009;58(1):86\u201393. https:\/\/doi.org\/10.1099\/jmm.0.000034-0.","journal-title":"J Med Microbiol"},{"issue":"1","key":"5329_CR28","doi-asserted-by":"publisher","first-page":"10484","DOI":"10.1038\/s41598-023-37307-6","volume":"13","author":"M Mohammed","year":"2023","unstructured":"Mohammed M, Casjens SR, Millard AD, Harrison C, Gannon L, Chattaway MA. Genomic analysis of Anderson typing phages of Salmonella Typhimrium: towards understanding the basis of bacteria-phage interaction. Sci Rep. 2023;13(1):10484. https:\/\/doi.org\/10.1038\/s41598-023-37307-6.","journal-title":"Sci Rep"},{"issue":"3","key":"5329_CR29","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1017\/S095026880003017X","volume":"102","author":"EJ Threlfall","year":"1989","unstructured":"Threlfall EJ, Rowe B, Ward LR. Subdivision of Salmonella enteritidis phage types by plasmid profile typing. Epidemiol Infect. 1989;102(3):459\u201365. https:\/\/doi.org\/10.1017\/S095026880003017X.","journal-title":"Epidemiol Infect"},{"issue":"1","key":"5329_CR30","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1186\/s13104-017-2878-0","volume":"10","author":"M Mohammed","year":"2017","unstructured":"Mohammed M. Phage typing or CRISPR typing for epidemiological surveillance of Salmonella Typhimurium? BMC Res Notes. 2017;10(1):578. https:\/\/doi.org\/10.1186\/s13104-017-2878-0.","journal-title":"BMC Res Notes"},{"issue":"9","key":"5329_CR31","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1111\/j.1348-0421.1995.tb03255.x","volume":"39","author":"T Murase","year":"1995","unstructured":"Murase T, Okitsu T, Suzuki R, Morozumi H, Matsushima A, Nakamura A, et al. Evaluation of DNA fingerprinting by PFGE as an epidemiologic tool for Salmonella infections. Microbiol Immunol. 1995;39(9):673\u20136. https:\/\/doi.org\/10.1111\/j.1348-0421.1995.tb03255.x.","journal-title":"Microbiol Immunol"},{"issue":"2","key":"5329_CR32","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/S0378-1135(00)00208-X","volume":"75","author":"I Laconcha","year":"2000","unstructured":"Laconcha I, Baggesen DL, Rementeria A, Garaizar J. Genotypic characterisation by PFGE of Salmonella enterica serotype Enteritidis phage types 1, 4, 6, and 8 isolated from animal and human sources in three European countries. Vet Microbiol. 2000;75(2):155\u201365. https:\/\/doi.org\/10.1016\/S0378-1135(00)00208-X.","journal-title":"Vet Microbiol"},{"issue":"4","key":"5329_CR33","doi-asserted-by":"publisher","first-page":"1617","DOI":"10.1128\/JCM.41.4.1617-1622.2003","volume":"41","author":"J Fernandez","year":"2003","unstructured":"Fernandez J, Fica A, Ebensperger G, Calfullan H, Prat S, Fernandez A, et al. Analysis of molecular epidemiology of Chilean Salmonella enterica serotype enteritidis isolates by pulsed-field gel electrophoresis and bacteriophage typing. J Clin Microbiol. 2003;41(4):1617\u201322. https:\/\/doi.org\/10.1128\/JCM.41.4.1617-1622.2003.","journal-title":"J Clin Microbiol"},{"issue":"8","key":"5329_CR34","doi-asserted-by":"publisher","first-page":"2314","DOI":"10.1128\/JCM.36.8.2314-2321.1998","volume":"36","author":"AM Ridley","year":"1998","unstructured":"Ridley AM, Threlfall EJ, Rowe B. Genotypic characterization of Salmonella enteritidis phage types by plasmid analysis, ribotyping, and pulsed-field gel electrophoresis. J Clin Microbiol. 1998;36(8):2314\u201321. https:\/\/doi.org\/10.1128\/JCM.36.8.2314-2321.1998.","journal-title":"J Clin Microbiol"},{"issue":"D1","key":"5329_CR35","doi-asserted-by":"publisher","first-page":"D757","DOI":"10.1093\/nar\/gkae902","volume":"53","author":"NP Dyer","year":"2025","unstructured":"Dyer NP, P\u00e4uker B, Baxter L, Gupta A, Bunk B, Overmann J, et al. EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens. Nucleic Acids Res. 2025;53(D1):D757\u201362. https:\/\/doi.org\/10.1093\/nar\/gkae902.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"5329_CR36","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.1038\/s41564-024-01832-5","volume":"9","author":"B Gaborieau","year":"2024","unstructured":"Gaborieau B, Vaysset H, Tesson F, Charachon I, Dib N, Bernier J, et al. Prediction of strain level phage-host interactions across the Escherichia genus using only genomic information. Nat Microbiol. 2024;9(11):2847\u201361. https:\/\/doi.org\/10.1038\/s41564-024-01832-5.","journal-title":"Nat Microbiol"},{"issue":"1","key":"5329_CR37","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1128\/jcm.35.1.330-333.1997","volume":"35","author":"DL Baggesen","year":"1997","unstructured":"Baggesen DL, Wegener HC, Madsen M. Correlation of conversion of Salmonella enterica serovar enteritidis phage type 1, 4, or 6 to phage type 7 with loss of lipopolysaccharide. J Clin Microbiol. 1997;35(1):330\u20133. https:\/\/doi.org\/10.1128\/jcm.35.1.330-333.1997.","journal-title":"J Clin Microbiol"},{"issue":"5","key":"5329_CR38","doi-asserted-by":"publisher","first-page":"1490","DOI":"10.1128\/JCM.00051-14","volume":"52","author":"J Zheng","year":"2014","unstructured":"Zheng J, Pettengill J, Strain E, Allard MW, Ahmed R, Zhao S, et al. Genetic diversity and evolution of Salmonella enterica serovar Enteritidis strains with different phage types. J Clin Microbiol. 2014;52(5):1490\u2013500. https:\/\/doi.org\/10.1128\/JCM.00051-14.","journal-title":"J Clin Microbiol"},{"issue":"15","key":"5329_CR39","doi-asserted-by":"publisher","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","volume":"34","author":"W De Coster","year":"2018","unstructured":"De Coster W, D\u2019Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018;34(15):2666\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/bty149.","journal-title":"Bioinformatics"},{"key":"5329_CR40","unstructured":"Wick R, (2018). Porechop: Adapter trimmer for Oxford Nanopore reads. GitHub. https:\/\/github.com\/rrwick\/Porechop"},{"issue":"1","key":"5329_CR41","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","volume":"20","author":"DE Wood","year":"2019","unstructured":"Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019;20(1):257. https:\/\/doi.org\/10.1186\/s13059-019-1891-0.","journal-title":"Genome Biol"},{"issue":"5","key":"5329_CR42","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","volume":"37","author":"M Kolmogorov","year":"2019","unstructured":"Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019;37(5):540\u20136. https:\/\/doi.org\/10.1038\/s41587-019-0072-8.","journal-title":"Nat Biotechnol"},{"issue":"5","key":"5329_CR43","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1038\/s43588-021-00073-4","volume":"1","author":"R Vaser","year":"2021","unstructured":"Vaser R, \u0160iki\u0107 M. Time- and memory-efficient genome assembly with Raven. Nat Comput Sci. 2021;1(5):332\u20136. https:\/\/doi.org\/10.1038\/s43588-021-00073-4.","journal-title":"Nat Comput Sci"},{"issue":"14","key":"5329_CR44","doi-asserted-by":"publisher","first-page":"2103","DOI":"10.1093\/bioinformatics\/btw152","volume":"32","author":"H Li","year":"2016","unstructured":"Li H. Minimap and miniasm: Fast mapping and de novo assembly for noisy long sequences. Bioinformatics. 2016;32(14):2103\u201310. https:\/\/doi.org\/10.1093\/bioinformatics\/btw152.","journal-title":"Bioinformatics"},{"issue":"8","key":"5329_CR45","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","volume":"29","author":"A Gurevich","year":"2013","unstructured":"Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: Quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072\u20135. https:\/\/doi.org\/10.1093\/bioinformatics\/btt086.","journal-title":"Bioinformatics"},{"key":"5329_CR46","unstructured":"Oxford Nanopore Technologies Ltd. (2018) Medaka. Sequence correction provided by ONT Research. Github. https:\/\/github.com\/nanoporetech\/medaka"},{"issue":"19","key":"5329_CR47","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","volume":"31","author":"FA Sim\u00e3o","year":"2015","unstructured":"Sim\u00e3o FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210\u20132. https:\/\/doi.org\/10.1093\/bioinformatics\/btv351.","journal-title":"Bioinformatics"},{"issue":"16","key":"5329_CR48","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment\/Map format and SAMtools. Bioinformatics (Oxford, England). 2009;25(16):2078\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/btp352.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"14","key":"5329_CR49","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/btu153.","journal-title":"Bioinformatics"},{"issue":"12","key":"5329_CR50","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"38","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra CP, Hern\u00e1ndez-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021;38(12):5825\u20139. https:\/\/doi.org\/10.1093\/molbev\/msab293.","journal-title":"Mol Biol Evol"},{"issue":"2","key":"5329_CR51","doi-asserted-by":"publisher","first-page":"e01064","DOI":"10.1128\/MRA.01064-19","volume":"9","author":"MZ Anwar","year":"2020","unstructured":"Anwar MZ, Zervas A, Hansen LH, Barker G, Anesio AM, Jacobsen CS. Complete genome and plasmid sequences of salmonella enterica subsp enterica Serovar Enteritidis PT1, obtained from the salmonella reference laboratory at public health England, Colindale United Kingdom. Microbiol Res Announce. 2020;9(2):e01064-e1119. https:\/\/doi.org\/10.1128\/MRA.01064-19.","journal-title":"Microbiol Res Announce"},{"key":"5329_CR52","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2164-12-402","volume":"12","author":"NF Alikhan","year":"2011","unstructured":"Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011;12:1\u201310. https:\/\/doi.org\/10.1186\/1471-2164-12-402.","journal-title":"BMC Genomics"},{"issue":"16","key":"5329_CR53","doi-asserted-by":"publisher","first-page":"3422","DOI":"10.1093\/bioinformatics\/bti553","volume":"21","author":"TJ Carver","year":"2005","unstructured":"Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. ACT: the Artemis Comparison Tool. Bioinformatics. 2005;21(16):3422\u20133. https:\/\/doi.org\/10.1093\/bioinformatics\/bti553.","journal-title":"Bioinformatics"},{"key":"5329_CR54","unstructured":"Seemann T. (2015). Snippy: fast bacterial variant calling from NGS reads [Computer software]. Retrieved from https:\/\/github.com\/tseemann\/snippy"},{"key":"5329_CR55","doi-asserted-by":"publisher","unstructured":"Wong TK, Ly-Trong N, Ren H, Ba\u00f1os H, Roger AJ, Susko E, Bielow C, De Maio N, Goldman N, Hahn MW, Huttley G, Lanfear R, Minh BQ, (2025). IQ-TREE 3: phylogenomic inference software using complex evolutionary models. https:\/\/doi.org\/10.32942\/X2P62N\/","DOI":"10.32942\/X2P62N"},{"issue":"6","key":"5329_CR56","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","volume":"14","author":"S Kalyaanamoorthy","year":"2017","unstructured":"Kalyaanamoorthy S, Minh BQ, Wong TK, Von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14(6):587\u20139. https:\/\/doi.org\/10.1038\/nmeth.4285.","journal-title":"Nat Methods"},{"issue":"2","key":"5329_CR57","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1093\/molbev\/msx281","volume":"35","author":"DT Hoang","year":"2018","unstructured":"Hoang DT, Chernomor O, Von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35(2):518\u201322. https:\/\/doi.org\/10.1093\/molbev\/msx281.","journal-title":"Mol Biol Evol"},{"issue":"2","key":"5329_CR58","doi-asserted-by":"publisher","first-page":"e1004041","DOI":"10.1371\/journal.pcbi.1004041","volume":"11","author":"X Didelot","year":"2015","unstructured":"Didelot X, Wilson DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol. 2015;11(2):e1004041. https:\/\/doi.org\/10.1371\/journal.pcbi.1004041.","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"5329_CR59","doi-asserted-by":"publisher","first-page":"2561","DOI":"10.1038\/s41467-022-30269-9","volume":"13","author":"F Tesson","year":"2022","unstructured":"Tesson F, Herv\u00e9 A, Mordret E, Touchon M, d\u2019Humi\u00e8res C, Cury J, et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat Commun. 2022;13(1):2561. https:\/\/doi.org\/10.1038\/s41467-022-30269-9.","journal-title":"Nat Commun"},{"key":"5329_CR60","doi-asserted-by":"publisher","unstructured":"Tesson, F.; Planel, R.; Egorov, A. A.; Georjon, H.; Vaysset, H.; Brancotte, B.; N\u00e9ron, B.; Mordret, E.; Atkinson, G. C.; Bernheim, A.; Cury, J. (2024). A comprehensive resource for exploring antiphage defense: defensefinder webservice, Wiki and Databases. Peer Community J 4(e91). https:\/\/doi.org\/10.24072\/pcjournal.470","DOI":"10.24072\/pcjournal.470"},{"key":"5329_CR61","doi-asserted-by":"publisher","unstructured":"N\u00e9ron B, Denise R, Coluzzi C, Touchon M, Rocha EPC, Abby SS, (2023). MacSyFinder v2: improved modelling and search engine to identify molecular systems in genomes. Peer Community J, 3(e28). https:\/\/doi.org\/10.24072\/pcjournal.250","DOI":"10.24072\/pcjournal.250"},{"key":"5329_CR62","doi-asserted-by":"publisher","first-page":"10868","DOI":"10.1093\/nar\/gkab883","volume":"49","author":"LJ Payne","year":"2021","unstructured":"Payne LJ, Todeschini TC, Wu Y, Perry BJ, Ronson CW, Fineran PC, et al. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Res. 2021;49:10868\u201378. https:\/\/doi.org\/10.1093\/nar\/gkab883.","journal-title":"Nucleic Acids Res"},{"key":"5329_CR63","doi-asserted-by":"publisher","first-page":"W541","DOI":"10.1093\/nar\/gkac400","volume":"50","author":"LJ Payne","year":"2022","unstructured":"Payne LJ, Meaden S, Mestre MR, Palmer C, Toro N, Fineran PC, et al. PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. Nucleic Acids Res. 2022;50:W541\u201350. https:\/\/doi.org\/10.1093\/nar\/gkac400.","journal-title":"Nucleic Acids Res"},{"key":"5329_CR64","doi-asserted-by":"crossref","unstructured":"Wickham H, (2016). ggplot2: elegant graphics for data analysis. Springer-Verlag New York. https:\/\/ggplot2.tidyverse.org","DOI":"10.1007\/978-3-319-24277-4_9"},{"issue":"4","key":"5329_CR65","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1089\/crispr.2022.0080","volume":"6","author":"AJ Collins","year":"2023","unstructured":"Collins AJ, Whitaker RJ. CRISPR comparison toolkit: rapid identification, visualization, and analysis of CRISPR array diversity. The CRISPR journal. 2023;6(4):386\u2013400. https:\/\/doi.org\/10.1089\/crispr.2022.0080.","journal-title":"The CRISPR journal"},{"key":"5329_CR66","doi-asserted-by":"publisher","first-page":"885048","DOI":"10.3389\/fgene.2022.885048","volume":"13","author":"R Gan","year":"2022","unstructured":"Gan R, Zhou F, Si Y, Yang H, Chen C, Ren C, et al. DBSCAN-SWA: an integrated tool for rapid prophage detection and annotation. Front Genet. 2022;13:885048. https:\/\/doi.org\/10.3389\/fgene.2022.885048.","journal-title":"Front Genet"},{"issue":"W1","key":"5329_CR67","doi-asserted-by":"publisher","first-page":"W443","DOI":"10.1093\/nar\/gkad382","volume":"51","author":"DS Wishart","year":"2023","unstructured":"Wishart DS, Han S, Saha S, Oler E, Peters H, Grant JR, et al. PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res. 2023;51(W1):W443\u201350. https:\/\/doi.org\/10.1093\/nar\/gkad382.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"5329_CR68","doi-asserted-by":"publisher","first-page":"830","DOI":"10.1093\/bioinformatics\/btac830","volume":"39","author":"JT Robinson","year":"2023","unstructured":"Robinson JT, Thorvaldsdottir H, Turner D, Mesirov JP. igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). Bioinformatics (Oxford, England). 2023;39(1):830. https:\/\/doi.org\/10.1093\/bioinformatics\/btac830.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"5","key":"5329_CR69","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1016\/j.ijantimicag.2005.02.006","volume":"25","author":"KL Hopkins","year":"2005","unstructured":"Hopkins KL, Davies RH, Threlfall EJ. Mechanisms of quinolone resistance in Escherichia coli and Salmonella: recent developments. Int J Antimicrob Agents. 2005;25(5):358\u201373. https:\/\/doi.org\/10.1016\/j.ijantimicag.2005.02.006.","journal-title":"Int J Antimicrob Agents"},{"issue":"4","key":"5329_CR70","doi-asserted-by":"publisher","first-page":"dlae127","DOI":"10.1093\/jacamr\/dlae127","volume":"6","author":"L Kherroubi","year":"2024","unstructured":"Kherroubi L, Bacon J, Rahman KM. Navigating fluoroquinolone resistance in Gram-negative bacteria: a comprehensive evaluation. JAC-Antimicrob Resist. 2024;6(4):dlae127. https:\/\/doi.org\/10.1093\/jacamr\/dlae127.","journal-title":"JAC-Antimicrob Resist"},{"issue":"10","key":"5329_CR71","doi-asserted-by":"publisher","first-page":"1624","DOI":"10.1101\/gr.077404.108","volume":"18","author":"NR Thomson","year":"2008","unstructured":"Thomson NR, Clayton DJ, Windhorst D, Vernikos G, Davidson S, Churcher C, et al. Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287\/91 provides insights into evolutionary and host adaptation pathways. Genome Res. 2008;18(10):1624\u201337. https:\/\/doi.org\/10.1101\/gr.077404.108.","journal-title":"Genome Res"},{"issue":"1","key":"5329_CR72","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1080\/09687680310001607369","volume":"21","author":"TH Plantinga","year":"2004","unstructured":"Plantinga TH, Van Der Does C, Badia J, Aguilar J, Konings WN, Driessen AJ. Functional characterization of the Escherichia coli K-12 yiaMNO transport protein genes. Mol Membr Biol. 2004;21(1):51\u20137. https:\/\/doi.org\/10.1080\/09687680310001607369.","journal-title":"Mol Membr Biol"},{"issue":"3","key":"5329_CR73","doi-asserted-by":"publisher","first-page":"113925","DOI":"10.1016\/j.celrep.2024.113925","volume":"43","author":"E G\u00fcl","year":"2024","unstructured":"G\u00fcl E, Huuskonen J, Abi Younes A, Maurer L, Enz U, Zimmermann J, et al. Salmonella T3SS-2 virulence enhances gut-luminal colonization by enabling chemotaxis-dependent exploitation of intestinal inflammation. Cell Rep. 2024;43(3):113925. https:\/\/doi.org\/10.1016\/j.celrep.2024.113925.","journal-title":"Cell Rep"},{"issue":"4","key":"5329_CR74","doi-asserted-by":"publisher","first-page":"652","DOI":"10.1016\/j.str.2025.01.014","volume":"33","author":"BJ Lane","year":"2025","unstructured":"Lane BJ, Dionysopoulou M, Yan N, Lippiat JD, Muench SP, Pliotas C. The mechanosensitive channel YbiO has a conductance equivalent to the largest gated pore. Structure (London, England: 1993). 2025;33(4):652\u201362. https:\/\/doi.org\/10.1016\/j.str.2025.01.014.","journal-title":"Structure (London, England: 1993)"},{"issue":"4","key":"5329_CR75","doi-asserted-by":"publisher","first-page":"871","DOI":"10.3382\/ps.2013-03710","volume":"93","author":"TM Addwebi","year":"2014","unstructured":"Addwebi TM, Call DR, Shah DH. Contribution of Salmonella Enteritidis virulence factors to intestinal colonization and systemic dissemination in 1-day-old chickens. Poult Sci. 2014;93(4):871\u201381. https:\/\/doi.org\/10.3382\/ps.2013-03710.","journal-title":"Poult Sci"},{"key":"5329_CR76","doi-asserted-by":"publisher","unstructured":"Chapman MR, Mulvey MA, Hultgren SJ, (2002). Fimbriae and pili. In M. Sussman (Ed.), Molecular medical microbiology (pp. 177\u2013197). Academic Press. https:\/\/doi.org\/10.1016\/B978-012677530-3\/50228-2","DOI":"10.1016\/B978-012677530-3\/50228-2"},{"issue":"8","key":"5329_CR77","doi-asserted-by":"publisher","first-page":"e43392","DOI":"10.1371\/journal.pone.0043392","volume":"7","author":"H Shin","year":"2012","unstructured":"Shin H, Lee JH, Kim H, Choi Y, Heu S, Ryu S. Receptor diversity and host interaction of bacteriophages infecting Salmonella enterica serovar Typhimurium. PLoS ONE. 2012;7(8):e43392. https:\/\/doi.org\/10.1371\/journal.pone.0043392.","journal-title":"PLoS ONE"},{"key":"5329_CR78","doi-asserted-by":"publisher","first-page":"442","DOI":"10.3389\/fmicb.2014.00442","volume":"5","author":"S Chaturongakul","year":"2014","unstructured":"Chaturongakul S, Ounjai P. Phage-host interplay: examples from tailed phages and Gram-negative bacterial pathogens. Front Microbiol. 2014;5:442. https:\/\/doi.org\/10.3389\/fmicb.2014.00442.","journal-title":"Front Microbiol"},{"issue":"9","key":"5329_CR79","doi-asserted-by":"publisher","first-page":"1348","DOI":"10.3390\/v16091348","volume":"16","author":"MJ Bucher","year":"2024","unstructured":"Bucher MJ, Czy\u017c DM. Phage against the machine: the SIE-ence of superinfection exclusion. Viruses. 2024;16(9):1348. https:\/\/doi.org\/10.3390\/v16091348.","journal-title":"Viruses"},{"issue":"3","key":"5329_CR80","doi-asserted-by":"publisher","first-page":"112","DOI":"10.31083\/j.fbl2903112","volume":"29","author":"J Liu","year":"2024","unstructured":"Liu J, Hou Y, Zhao L, Chen G, Chen J, Zhao Q, et al. Antimicrobial resistance and the genomic epidemiology of multidrug-resistant\u00a0Salmonella enterica\u00a0serovar Enteritidis ST11 in China. Front Biosci (Landmark edition). 2024;29(3):112. https:\/\/doi.org\/10.31083\/j.fbl2903112.","journal-title":"Front Biosci (Landmark edition)"},{"issue":"3","key":"5329_CR81","doi-asserted-by":"publisher","first-page":"951","DOI":"10.1093\/genetics\/165.3.951","volume":"165","author":"RA Helm","year":"2003","unstructured":"Helm RA, Lee AG, Christman HD, Maloy S. Genomic rearrangements at rrn operons in Salmonella. Genetics. 2003;165(3):951\u20139. https:\/\/doi.org\/10.1093\/genetics\/165.3.951.","journal-title":"Genetics"},{"issue":"2","key":"5329_CR82","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1128\/jb.147.2.452-462.1981","volume":"147","author":"DL Blazey","year":"1981","unstructured":"Blazey DL, Kim R, Burns RO. Molecular cloning and expression of the ilvGEDAY genes from Salmonella typhimurium. J Bacteriol. 1981;147(2):452\u201362. https:\/\/doi.org\/10.1128\/jb.147.2.452-462.1981.","journal-title":"J Bacteriol"},{"issue":"4","key":"5329_CR83","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1021\/acschembio.0c00983","volume":"16","author":"CR Eade","year":"2021","unstructured":"Eade CR, Wallen TW, Gates CE, Oliverio CL, Scarbrough BA, Reid AJ, et al. Making the enterobacterial common antigen glycan and measuring its substrate sequestration. ACS Chem Biol. 2021;16(4):691\u2013700. https:\/\/doi.org\/10.1021\/acschembio.0c00983.","journal-title":"ACS Chem Biol"},{"issue":"4","key":"5329_CR84","doi-asserted-by":"publisher","first-page":"e01914","DOI":"10.1128\/mBio.01914-20","volume":"11","author":"AK Rai","year":"2020","unstructured":"Rai AK, Mitchell AM. Enterobacterial common antigen: Synthesis and function of an enigmatic molecule. MBio. 2020;11(4):e01914-e1920. https:\/\/doi.org\/10.1128\/mBio.01914-20.","journal-title":"MBio"},{"key":"5329_CR85","doi-asserted-by":"publisher","first-page":"880932","DOI":"10.3389\/fmicb.2022.880932","volume":"13","author":"S Ojima","year":"2022","unstructured":"Ojima S, Ono HK, Okimoto R, Yu X, Sugiyama M, Yoshioka K, et al. wecB gene of Salmonella Gallinarum plays a critical role in systemic infection of fowl typhoid. Front Microbiol. 2022;13:880932. https:\/\/doi.org\/10.3389\/fmicb.2022.880932.","journal-title":"Front Microbiol"},{"issue":"3","key":"5329_CR86","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1111\/mmi.13936","volume":"108","author":"K Bohm","year":"2018","unstructured":"Bohm K, Porwollik S, Chu W, Dover JA, Gilcrease EB, Casjens SR, et al. Genes affecting progression of bacteriophage P22 infection in Salmonella identified by transposon and single gene deletion screens. Mol Microbiol. 2018;108(3):288\u2013305. https:\/\/doi.org\/10.1111\/mmi.13936.","journal-title":"Mol Microbiol"},{"key":"5329_CR87","doi-asserted-by":"publisher","first-page":"102321","DOI":"10.1016\/j.mib.2023.102321","volume":"73","author":"PH Patel","year":"2023","unstructured":"Patel PH, Maxwell KL. Prophages provide a rich source of antiphage defense systems. Curr Opin Microbiol. 2023;73:102321. https:\/\/doi.org\/10.1016\/j.mib.2023.102321.","journal-title":"Curr Opin Microbiol"},{"issue":"24","key":"5329_CR88","doi-asserted-by":"publisher","first-page":"13316","DOI":"10.3390\/ijms252413316","volume":"25","author":"X Xu","year":"2024","unstructured":"Xu X, Gu P. Overview of phage defense systems in bacteria and their applications. Int J Mol Sci. 2024;25(24):13316. https:\/\/doi.org\/10.3390\/ijms252413316.","journal-title":"Int J Mol Sci"},{"issue":"6793","key":"5329_CR89","doi-asserted-by":"publisher","first-page":"eadv7924","DOI":"10.1126\/science.adv7924","volume":"392","author":"PC DeWeirdt","year":"2026","unstructured":"DeWeirdt PC, Mahoney EM, Laub MT. DefensePredictor: A machine learning model to discover prokaryotic immune systems. Science (New York, NY). 2026;392(6793):eadv7924. https:\/\/doi.org\/10.1126\/science.adv7924.","journal-title":"Science (New York, NY)"},{"issue":"6747","key":"5329_CR90","doi-asserted-by":"publisher","first-page":"eads0768","DOI":"10.1126\/science.ads0768","volume":"388","author":"B Darracq","year":"2025","unstructured":"Darracq B, Littner E, Brunie M, Bos J, Kaminski PA, Depardieu F, et al. Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems. Science (New York, NY). 2025;388(6747):eads0768. https:\/\/doi.org\/10.1126\/science.ads0768.","journal-title":"Science (New York, NY)"},{"issue":"6","key":"5329_CR91","doi-asserted-by":"publisher","first-page":"1421","DOI":"10.1046\/j.1365-2958.2002.02989.x","volume":"44","author":"AS Bhagwat","year":"2002","unstructured":"Bhagwat AS, Lieb M. Cooperation and competition in mismatch repair: very short-patch repair and methyl-directed mismatch repair in Escherichia coli. Mol Microbiol. 2002;44(6):1421\u20138. https:\/\/doi.org\/10.1046\/j.1365-2958.2002.02989.x.","journal-title":"Mol Microbiol"},{"issue":"6","key":"5329_CR92","doi-asserted-by":"publisher","first-page":"3348","DOI":"10.1093\/nar\/gkac147","volume":"50","author":"N Birkholz","year":"2022","unstructured":"Birkholz N, Jackson SA, Fagerlund RD, Fineran PC. A mobile restriction-modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease. Nucleic Acids Res. 2022;50(6):3348\u201361. https:\/\/doi.org\/10.1093\/nar\/gkac147.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"5329_CR93","doi-asserted-by":"publisher","first-page":"330","DOI":"10.52601\/bpr.2025.240070","volume":"11","author":"H Kang","year":"2025","unstructured":"Kang H, Gao A, Zhu Y. Bacterial restriction-modification systems: mechanisms of defense against phage infection. Biophys Rep. 2025;11(5):330\u201343. https:\/\/doi.org\/10.52601\/bpr.2025.240070.","journal-title":"Biophys Rep"}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12866-026-05329-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-026-05329-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-026-05329-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T12:03:25Z","timestamp":1791806605000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12866-026-05329-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,11]]},"references-count":93,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["5329"],"URL":"https:\/\/doi.org\/10.1186\/s12866-026-05329-5","relation":{},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,11]]},"assertion":[{"value":"23 February 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 July 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"878"}}