{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:35:10Z","timestamp":1787009710182,"version":"build-2736575974"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2020,6,22]],"date-time":"2020-06-22T00:00:00Z","timestamp":1592784000000},"content-version":"vor","delay-in-days":173,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Filamentous phages establish chronic infections in their bacterial hosts, and new phages are secreted by infected bacteria for multiple generations, typically without causing host death. Often, these viruses integrate in their host\u2019s genome by co-opting the host\u2019s XerCD recombinase system. In several cases, these viruses also encode genes that increase bacterial virulence in plants and animals. Here, we describe a new filamentous phage, UP\u03d5901, which we originally found integrated in a clinical isolate of Escherichia coli from urine. UP\u03d5901 and closely related phages can be found in published genomes of over 200 other bacteria, including strains of Citrobacter koseri, Salmonella enterica, Yersinia enterocolitica, and Klebsiella pneumoniae. Its closest relatives are consistently found in urine or in the blood and feces of patients with urinary tract infections. More distant relatives can be found in isolates from other environments, including sewage, water, soil, and contaminated food. Each of these phages, which we collectively call \u2018UP\u03d5 viruses\u2019, also harbors two or more novel genes of unknown function.<\/jats:p>","DOI":"10.1093\/ve\/veaa030","type":"journal-article","created":{"date-parts":[[2020,4,15]],"date-time":"2020-04-15T15:24:59Z","timestamp":1586964299000},"source":"Crossref","is-referenced-by-count":14,"title":["UP\u03a6\u00a0phages, a new group of filamentous phages found in several members of Enterobacteriales"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1321-8418","authenticated-orcid":false,"given":"Jason W","family":"Shapiro","sequence":"first","affiliation":[{"name":"Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Putonti","sequence":"additional","affiliation":[{"name":"Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA"},{"name":"Department of Computer Science, Loyola University Chicago, 1052 W Loyola Ave, Chicago, IL, 60626, USA"},{"name":"Bioinformatics Program, Loyola University Chicago, 1052 W Loyola Ave, Chicago, IL 60626, USA"},{"name":"Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, 2160 S First Ave, Maywood, IL 60153, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,6,22]]},"reference":[{"key":"2020072707365120100_veaa030-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic Local Alignment Search Tool","volume":"215","author":"Altschul","year":"1990","journal-title":"Journal of Molecular Biology"},{"key":"2020072707365120100_veaa030-B2","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: A Better, Faster Version of the PHAST Phage Search 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