{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T14:33:34Z","timestamp":1793198014326,"version":"4.5.0"},"reference-count":82,"publisher":"Elsevier BV","issue":"12","license":[{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T00:00:00Z","timestamp":1765411200000},"content-version":"vor","delay-in-days":375,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","award":["1F31AI176589-01"],"award-info":[{"award-number":["1F31AI176589-01"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000861","name":"Burroughs Wellcome Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000861","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Host & Microbe"],"published-print":{"date-parts":[[2024,12]]},"DOI":"10.1016\/j.chom.2024.10.012","type":"journal-article","created":{"date-parts":[[2024,11,7]],"date-time":"2024-11-07T09:32:32Z","timestamp":1730971952000},"page":"2063-2079.e8","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":33,"title":["A prophage competition element protects Salmonella from lysis"],"prefix":"10.1016","volume":"32","author":[{"given":"Molly R.","family":"Sargen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9877-4180","authenticated-orcid":false,"given":"Sophie","family":"Helaine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.chom.2024.10.012_bib1","series-title":"Phages: Their Role in Bacterial Pathogenesis and Biotechnology","author":"Waldor","year":"2005"},{"key":"10.1016\/j.chom.2024.10.012_bib2","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1111\/mmi.12933","article-title":"A BTP1 prophage gene present in invasive non-typhoidal Salmonella determines composition and length of the O-antigen of the lipopolysaccharide","volume":"96","author":"Kintz","year":"2015","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2024.10.012_bib3","doi-asserted-by":"crossref","first-page":"1568","DOI":"10.1038\/s41564-022-01219-4","article-title":"A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome","volume":"7","author":"Vassallo","year":"2022","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2024.10.012_bib4","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1128\/jb.177.3.497-501.1995","article-title":"The old exonuclease of bacteriophage P2","volume":"177","author":"Myung","year":"1995","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.chom.2024.10.012_bib5","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1016\/j.chom.2022.02.018","article-title":"Phages and their satellites encode hotspots of antiviral systems","volume":"30","author":"Rousset","year":"2022","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2024.10.012_bib6","doi-asserted-by":"crossref","first-page":"2854","DOI":"10.1038\/ismej.2016.79","article-title":"Prophages mediate defense against phage infection through diverse mechanisms","volume":"10","author":"Bondy-Denomy","year":"2016","journal-title":"ISME J."},{"key":"10.1016\/j.chom.2024.10.012_bib7","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1146\/annurev.genet.39.073003.113656","article-title":"Switches in bacteriophage lambda development","volume":"39","author":"Oppenheim","year":"2005","journal-title":"Annu. Rev. Genet."},{"key":"10.1016\/j.chom.2024.10.012_bib8","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1111\/j.1365-2958.1993.tb01184.x","article-title":"Recombination-deficient mutants of Salmonella typhimurium are avirulent and sensitive to the oxidative burst of macrophages","volume":"7","author":"Buchmeier","year":"1993","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2024.10.012_bib9","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1128\/MMBR.68.3.560-602.2004","article-title":"Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion","volume":"68","author":"Br\u00fcssow","year":"2004","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.chom.2024.10.012_bib10","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1111\/mmi.14167","article-title":"Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host?","volume":"111","author":"Wahl","year":"2019","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2024.10.012_bib11","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1007494","article-title":"Prophage induction, but not production of phage particles, is required for lethal disease in a microbiome-replete murine model of enterohemorrhagic E. coli infection","volume":"15","author":"Balasubramanian","year":"2019","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.chom.2024.10.012_bib12","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1016\/j.cell.2012.06.036","article-title":"Prophage excision activates Listeria competence genes that promote phagosomal escape and virulence","volume":"150","author":"Rabinovich","year":"2012","journal-title":"Cell"},{"key":"10.1016\/j.chom.2024.10.012_bib13","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.107956","article-title":"Active Lysogeny in Listeria Monocytogenes Is a Bacteria-Phage Adaptive Response in the Mammalian Environment","volume":"32","author":"Pasechnek","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.chom.2024.10.012_bib14","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1011127","article-title":"Phage production is blocked in the adherent-invasive Escherichia coli LF82 upon macrophage infection","volume":"19","author":"Misson","year":"2023","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.chom.2024.10.012_bib15","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1126\/science.1244705","article-title":"Internalization of Salmonella by macrophages induces formation of nonreplicating persisters","volume":"343","author":"Helaine","year":"2014","journal-title":"Science"},{"key":"10.1016\/j.chom.2024.10.012_bib16","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1099\/mic.0.000288","article-title":"Elucidating population-wide mycobacterial replication dynamics at the single-cell level","volume":"162","author":"Mouton","year":"2016","journal-title":"Microbiology (Reading)"},{"key":"10.1016\/j.chom.2024.10.012_bib17","doi-asserted-by":"crossref","first-page":"2200","DOI":"10.1038\/s41467-020-15966-7","article-title":"Intracellular Staphylococcus aureus persisters upon antibiotic exposure","volume":"11","author":"Peyrusson","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2024.10.012_bib18","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1016\/j.chom.2021.10.002","article-title":"The vulnerable versatility of Salmonella antibiotic persisters during infection","volume":"29","author":"Hill","year":"2021","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2024.10.012_bib19","doi-asserted-by":"crossref","first-page":"4038","DOI":"10.1128\/JB.186.12.4038-4041.2004","article-title":"Resuscitation of a defective prophage in Salmonella cocultures","volume":"186","author":"Figueroa-Bossi","year":"2004","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.chom.2024.10.012_bib20","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1046\/j.1365-2958.2001.02234.x","article-title":"Variable assortment of prophages provides a transferable repertoire of pathogenic determinants in Salmonella","volume":"39","author":"Figueroa-Bossi","year":"2001","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2024.10.012_bib21","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1046\/j.1365-2958.1999.01461.x","article-title":"Inducible prophages contribute to Salmonella virulence in mice","volume":"33","author":"Figueroa-Bossi","year":"1999","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2024.10.012_bib22","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1073\/pnas.0809600106","article-title":"Killing niche competitors by remote-control bacteriophage induction","volume":"106","author":"Selva","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2024.10.012_bib23","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1128\/AAC.40.6.1561","article-title":"Sensitization of bacteria to danofloxacin by temperate prophages","volume":"40","author":"Froshauer","year":"1996","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.chom.2024.10.012_bib24","doi-asserted-by":"crossref","first-page":"778","DOI":"10.3390\/ph8040778","article-title":"Non-Monotonic Survival of Staphylococcus aureus with Respect to Ciprofloxacin Concentration Arises from Prophage-Dependent Killing of Persisters","volume":"8","author":"Sandvik","year":"2015","journal-title":"Pharmaceuticals (Basel)"},{"key":"10.1016\/j.chom.2024.10.012_bib25","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.01874-23","article-title":"Prophage Gifsy-1 Induction in Salmonella enterica Serovar Typhimurium Reduces Persister Cell Formation after Ciprofloxacin Exposure","volume":"11","author":"Braetz","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"10.1016\/j.chom.2024.10.012_bib26","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1016\/j.chom.2013.11.010","article-title":"An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium","volume":"14","author":"Kr\u00f6ger","year":"2013","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2024.10.012_bib27","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.01024-16","article-title":"Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion","volume":"7","author":"Smith","year":"2016","journal-title":"mBio"},{"key":"10.1016\/j.chom.2024.10.012_bib28","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1073\/pnas.66.3.587","article-title":"Bacteriophage lambda; abortive infection of bacteria lysogenic for phage P2","volume":"66","author":"Lindahl","year":"1970","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2024.10.012_bib29","doi-asserted-by":"crossref","first-page":"2361","DOI":"10.1016\/j.molcel.2021.03.027","article-title":"Shutoff of host transcription triggers a toxin-antitoxin system to cleave phage RNA and abort infection","volume":"81","author":"Guegler","year":"2021","journal-title":"Mol. Cell"},{"key":"10.1016\/j.chom.2024.10.012_bib30","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btaa788","article-title":"FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation","volume":"37","author":"Saha","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2024.10.012_bib31","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1002149","article-title":"Bacteriophage crosstalk: coordination of prophage induction by trans-acting antirepressors","volume":"7","author":"Lemire","year":"2011","journal-title":"PLoS Genet."},{"key":"10.1016\/j.chom.2024.10.012_bib32","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1038\/ismej.2011.30","article-title":"Within-host competition determines reproductive success of temperate bacteriophages","volume":"5","author":"Refardt","year":"2011","journal-title":"ISME J."},{"key":"10.1016\/j.chom.2024.10.012_bib33","doi-asserted-by":"crossref","first-page":"17823","DOI":"10.1074\/jbc.M113.469981","article-title":"Dissection of the ATPase active site of P1 ParA reveals multiple active forms essential for plasmid partition","volume":"288","author":"Vecchiarelli","year":"2013","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.chom.2024.10.012_bib34","doi-asserted-by":"crossref","first-page":"4901","DOI":"10.1093\/emboj\/20.17.4901","article-title":"Probing the ATP-binding site of P1 ParA: partition and repression have different requirements for ATP binding and hydrolysis","volume":"20","author":"Fung","year":"2001","journal-title":"EMBO J."},{"key":"10.1016\/j.chom.2024.10.012_bib35","doi-asserted-by":"crossref","first-page":"2113","DOI":"10.1093\/nar\/gky1251","article-title":"Crystal structures of HpSoj-DNA complexes and the nucleoid-adaptor complex formation in chromosome segregation","volume":"47","author":"Chu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2024.10.012_bib36","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.chom.2024.10.012_bib37","doi-asserted-by":"crossref","DOI":"10.1002\/pro.4519","article-title":"DALI shines a light on remote homologs: One hundred discoveries","volume":"32","author":"Holm","year":"2023","journal-title":"Protein Sci."},{"key":"10.1016\/j.chom.2024.10.012_bib38","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/1745-6150-8-15","article-title":"Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing","volume":"8","author":"Anantharaman","year":"2013","journal-title":"Biol. Direct"},{"key":"10.1016\/j.chom.2024.10.012_bib39","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1080\/10409238.2020.1856769","article-title":"HEPN RNases - an emerging class of functionally distinct RNA processing and degradation enzymes","volume":"56","author":"Pillon","year":"2021","journal-title":"Crit. Rev. Biochem. Mol. Biol."},{"key":"10.1016\/j.chom.2024.10.012_bib40","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.mib.2017.02.003","article-title":"Toxin-antitoxin systems: reversible toxicity","volume":"36","author":"Hall","year":"2017","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.chom.2024.10.012_bib41","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.ymeth.2007.10.006","article-title":"The many applications of acid urea polyacrylamide gel electrophoresis to studies of tRNAs and aminoacyl-tRNA synthetases","volume":"44","author":"K\u00f6hrer","year":"2008","journal-title":"Methods"},{"key":"10.1016\/j.chom.2024.10.012_bib42","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.molcel.2016.05.002","article-title":"A Salmonella Toxin Promotes Persister Formation through Acetylation of tRNA","volume":"63","author":"Cheverton","year":"2016","journal-title":"Mol. Cell"},{"key":"10.1016\/j.chom.2024.10.012_bib43","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1038\/90802","article-title":"Cell-free translation reconstituted with purified components","volume":"19","author":"Shimizu","year":"2001","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.chom.2024.10.012_bib44","doi-asserted-by":"crossref","first-page":"3209","DOI":"10.1093\/nar\/gkl415","article-title":"PrrC-anticodon nuclease: functional organization of a prototypical bacterial restriction RNase","volume":"34","author":"Blanga-Kanfi","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2024.10.012_bib45","doi-asserted-by":"crossref","first-page":"1560","DOI":"10.1111\/j.1365-2958.2008.06387.x","article-title":"RloC: a wobble nucleotide-excising and zinc-responsive bacterial tRNase","volume":"69","author":"Davidov","year":"2008","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2024.10.012_bib46","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1038\/s41589-020-0558-1","article-title":"Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications","volume":"16","author":"Kimura","year":"2020","journal-title":"Nat. Chem. Biol."},{"key":"10.1016\/j.chom.2024.10.012_bib47","doi-asserted-by":"crossref","first-page":"3746","DOI":"10.1073\/pnas.1000041107","article-title":"Dynamics of intracellular bacterial replication at the single cell level","volume":"107","author":"Helaine","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2024.10.012_bib48","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00065-13","article-title":"Identification of salmonella pathogenicity island-2 type III secretion system effectors involved in intramacrophage replication of S. enterica serovar typhimurium: implications for rational vaccine design","volume":"4","author":"Figueira","year":"2013","journal-title":"mBio"},{"key":"10.1016\/j.chom.2024.10.012_bib49","doi-asserted-by":"crossref","first-page":"1156","DOI":"10.1126\/science.aat7148","article-title":"Salmonella persisters undermine host immune defenses during antibiotic treatment","volume":"362","author":"Stapels","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.chom.2024.10.012_bib50","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.chom.2019.11.002","article-title":"Salmonella Effector SteE Converts the Mammalian Serine\/Threonine Kinase GSK3 into a Tyrosine Kinase to Direct Macrophage Polarization","volume":"27","author":"Panagi","year":"2020","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2024.10.012_bib51","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2022.110723","article-title":"A dual-function phage regulator controls the response of cohabiting phage elements via regulation of the bacterial SOS response","volume":"39","author":"Azulay","year":"2022","journal-title":"Cell Rep."},{"key":"10.1016\/j.chom.2024.10.012_bib52","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1038\/s41586-023-06376-y","article-title":"Small protein modules dictate prophage fates during polylysogeny","volume":"620","author":"Silpe","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.chom.2024.10.012_bib53","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1011363","article-title":"Induction mechanisms and strategies underlying interprophage competition during polylysogeny","volume":"19","author":"Silpe","year":"2023","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.chom.2024.10.012_bib54","doi-asserted-by":"crossref","first-page":"1620","DOI":"10.1016\/j.chom.2021.09.002","article-title":"Prophages encode phage-defense systems with cognate self-immunity","volume":"29","author":"Owen","year":"2021","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2024.10.012_bib55","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1126\/science.adl3222","article-title":"Prophage terminase with tRNase activity sensitizes Salmonella enterica to oxidative stress","volume":"384","author":"Uppalapati","year":"2024","journal-title":"Science"},{"key":"10.1016\/j.chom.2024.10.012_bib56","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.108527","article-title":"An RNA Repair Operon Regulated by Damaged tRNAs","volume":"33","author":"Hughes","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.chom.2024.10.012_bib57","doi-asserted-by":"crossref","DOI":"10.1128\/jb.00262-22","article-title":"Strain-Specific Gifsy-1 Prophage Genes Are Determinants for Expression of the RNA Repair Operon during the SOS Response in Salmonella enterica Serovar Typhimurium","volume":"205","author":"Kurasz","year":"2023","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.chom.2024.10.012_bib58","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1016\/j.chom.2024.05.010","article-title":"Tactical terminase: How a Salmonella prophage navigates oxidative stress","volume":"32","author":"Svenningsen","year":"2024","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2024.10.012_bib59","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/nature11433","article-title":"Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11","volume":"491","author":"Li","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.chom.2024.10.012_bib60","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1146\/annurev-genet-022620-101840","article-title":"Noncanonical Roles of tRNAs: tRNA Fragments and Beyond","volume":"54","author":"Su","year":"2020","journal-title":"Annu. Rev. Genet."},{"key":"10.1016\/j.chom.2024.10.012_bib61","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.chom.2017.07.009","article-title":"Salmonella SPI-2 Type III Secretion System Effectors: Molecular Mechanisms And Physiological Consequences","volume":"22","author":"Jennings","year":"2017","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2024.10.012_bib72","doi-asserted-by":"crossref","first-page":"D159","DOI":"10.1093\/nar\/gkn772","article-title":"tRNAdb 2009: compilation of tRNA sequences and tRNA genes","volume":"37","author":"J\u00fchling","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2024.10.012_bib73","article-title":"Aligning short sequencing reads with Bowtie","volume":"Chapter 11","author":"Langmead","year":"2010","journal-title":"Curr Protoc Bioinformatics"},{"key":"10.1016\/j.chom.2024.10.012_bib74","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2024.10.012_bib75","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2024.10.012_bib77","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2024.10.012_bib76","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2024.10.012_bib78","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.chom.2024.10.012_bib79","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2024.10.012_bib80","doi-asserted-by":"crossref","first-page":"3710","DOI":"10.1093\/bioinformatics\/bth456","article-title":"GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes","volume":"20","author":"Boyle","year":"2004","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2024.10.012_bib71","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH Image to ImageJ: 25 years of image analysis","volume":"9","author":"Schneider","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.chom.2024.10.012_bib62","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1046\/j.1365-2958.1999.01527.x","article-title":"PH-dependent secretion of SseB, a product of the SPI-2 type III secretion system of Salmonella typhimurium","volume":"33","author":"Beuz\u00f3n","year":"1999","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2024.10.012_bib63","doi-asserted-by":"crossref","first-page":"6640","DOI":"10.1073\/pnas.120163297","article-title":"One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products","volume":"97","author":"Datsenko","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2024.10.012_bib64","article-title":"Working with phage P22","volume":"2022","author":"Figueroa-Bossi","year":"2022","journal-title":"Cold Spring Harb. Protoc."},{"key":"10.1016\/j.chom.2024.10.012_bib65","doi-asserted-by":"crossref","DOI":"10.1128\/AEM.00990-19","article-title":"A New Suite of Allelic-Exchange Vectors for the Scarless Modification of Proteobacterial Genomes","volume":"85","author":"Lazarus","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.chom.2024.10.012_bib66","doi-asserted-by":"crossref","first-page":"6418","DOI":"10.1128\/JB.00621-10","article-title":"Silent mischief: bacteriophage Mu insertions contaminate products of Escherichia coli random mutagenesis performed using suicidal transposon delivery plasmids mobilized by broad-host-range RP4 conjugative machinery","volume":"192","author":"Ferri\u00e8res","year":"2010","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.chom.2024.10.012_bib67","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1128\/JB.187.3.1091-1104.2005","article-title":"The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy","volume":"187","author":"Casjens","year":"2005","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.chom.2024.10.012_bib68","doi-asserted-by":"crossref","first-page":"2607","DOI":"10.1093\/nar\/29.12.2607","article-title":"GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions","volume":"29","author":"Besemer","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2024.10.012_bib69","doi-asserted-by":"crossref","first-page":"1993","DOI":"10.1038\/s41467-018-04472-6","article-title":"Activity of acetyltransferase toxins involved in Salmonella persister formation during macrophage infection","volume":"9","author":"Rycroft","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2024.10.012_bib70","doi-asserted-by":"crossref","first-page":"1857","DOI":"10.1002\/prot.24364","article-title":"Optimized E. coli expression strain LOBSTR eliminates common contaminants from His-tag purification","volume":"81","author":"Andersen","year":"2013","journal-title":"Proteins"},{"key":"10.1016\/j.chom.2024.10.012_bib81","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1007\/978-1-4939-2854-5_15","article-title":"Analysis of Macrophage-Induced Salmonella Persisters","volume":"1333","author":"Fisher","year":"2016","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.chom.2024.10.012_bib82","doi-asserted-by":"crossref","first-page":"710","DOI":"10.3390\/v2030710","article-title":"Complete genomic sequence of bacteriophage felix o1","volume":"2","author":"Whichard","year":"2010","journal-title":"Viruses"}],"container-title":["Cell Host & Microbe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312824003986?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312824003986?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T00:36:31Z","timestamp":1765413391000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1931312824003986"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12]]},"references-count":82,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2024,12]]}},"alternative-id":["S1931312824003986"],"URL":"https:\/\/doi.org\/10.1016\/j.chom.2024.10.012","relation":{},"ISSN":["1931-3128"],"issn-type":[{"value":"1931-3128","type":"print"}],"subject":[],"published":{"date-parts":[[2024,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A prophage competition element protects Salmonella from lysis","name":"articletitle","label":"Article Title"},{"value":"Cell Host & Microbe","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.chom.2024.10.012","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 Elsevier Inc.","name":"copyright","label":"Copyright"}]}}