{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T10:50:17Z","timestamp":1767178217261,"version":"build-2238731810"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1005931","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,2,12]],"date-time":"2018-02-12T00:00:00Z","timestamp":1518393600000}}],"reference-count":35,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2018,1,31]],"date-time":"2018-01-31T00:00:00Z","timestamp":1517356800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004063","name":"Knut och Alice Wallenbergs Stiftelse","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004063","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004384","name":"Instytut Biologii Medycznej Polskiej Akademii Nauk","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004384","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004063","name":"Knut och Alice Wallenbergs Stiftelse","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004063","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005931","type":"journal-article","created":{"date-parts":[[2018,1,31]],"date-time":"2018-01-31T13:25:51Z","timestamp":1517405151000},"page":"e1005931","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Predicting pathogenicity behavior in Escherichia coli population through a state dependent model and TRS profiling"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5816-4345","authenticated-orcid":true,"given":"Krzysztof","family":"Bartoszek","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marta","family":"Majchrzak","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebastian","family":"Sakowski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna B.","family":"Kubiak-Szeligowska","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ingemar","family":"Kaj","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9074-2758","authenticated-orcid":true,"given":"Pawel","family":"Parniewski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2018,1,31]]},"reference":[{"key":"ref1","article-title":"Escherichia coli, Pathotypes and Principles of Pathogenesis","author":"M. S Donnenberg","year":"2013"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1707","DOI":"10.1111\/j.1462-5822.2006.00794.x","article-title":"Pathogenicity islands: a molecular toolbox for bacterial virulence","volume":"8","author":"O Gal-Mor","year":"2006","journal-title":"Cell Microbiol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1128\/CMR.17.1.14-56.2004","article-title":"Pathogenicity islands in bacterial pathogenesis","volume":"17","author":"H Schmidt","year":"2004","journal-title":"Clin Microbiol Rev"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4615-0117-6_1","article-title":"Molecular mechanisms of TRS instability","volume":"516","author":"P Parniewski","year":"2002","journal-title":"Adv Exp Med Biol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1016\/0959-437X(94)90067-1","article-title":"Simple sequences","volume":"4","author":"D Tautz","year":"1994","journal-title":"Curr Opin Genet Dev"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"7121","DOI":"10.1007\/s11033-014-3592-9","article-title":"TRS-based PCR as a potential tool for inter-serovar discrimination of Salmonella Enteritidis, S. Typhimurium, S. Infantis, S. Virchow, S. Hadar, S. Newport and S. Anatum","volume":"41","author":"M Majchrzak","year":"2014","journal-title":"Mol Biol Rep"},{"key":"ref7","article-title":"Trinucleotide Repeat Sequence-based PCR as a Potential Approach for Genotyping Mycobacterium gordonae strains","author":"A Wojtasik","year":"2011","journal-title":"J Microbiol Meth"},{"key":"ref8","article-title":"Comparison of the (CCG)4-based PCR and MIRU-VNTR for molecular typing of Mycobacterium avium strains","author":"A Wojtasik","year":"2012","journal-title":"Mol Biol Rep"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"3937","DOI":"10.1128\/JCM.01036-09","article-title":"(CGG)4-based PCR as a novel tool for discrimination of uropathogenic Escherichia coli strains: comparison with enterobacterial repetitive intergenic consensus-PCR","volume":"47","author":"W Adamus-Bialek","year":"2009","journal-title":"J Clin Microbiol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1007\/s11033-016-4031-x","article-title":"TRS-PCR profiling for discrimination of Escherichia coli strains isolated from children with diarrhea under 5 years of age in Lodz region, Poland","volume":"43","author":"AB Kubiak-Szeligowska","year":"2016","journal-title":"Mol Biol Rep"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1080\/10635150701607033","article-title":"Estimating a binary character's effect on speciation and extinction","volume":"56","author":"WP Maddison","year":"2007","journal-title":"Syst Biol"},{"key":"ref12","first-page":"07028","article-title":"Exact solution of a two-type branching process: clone size distribution in cell division kinetics","volume":"7","author":"T Antal","year":"2010","journal-title":"JSMTE"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1093\/sysbio\/syq053","article-title":"Quantitative Traits and Diversification","volume":"59","author":"RG FitzJohn","year":"2010","journal-title":"Syst Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1111\/j.2041-210X.2012.00234.x","article-title":"Diversitree: comparative phylogenetic analyses of diversication in R","volume":"3","author":"RG FitzJohn","year":"2012","journal-title":"Methods Ecol Evol"},{"key":"ref15","article-title":"R: A Language and Environment for Statistical Computing","year":"2016","journal-title":"R: A Language and Environment for Statistical Computing"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1093\/sysbio\/syw022","article-title":"Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction","volume":"65","author":"JM Beaulieu","year":"2016","journal-title":"Syst Biol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.spa.2003.12.002","article-title":"Functional limit theorems for multitype branching processes and generalized polya urns","volume":"110","author":"S Janson","year":"2004","journal-title":"Stoch Proc Appl"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1086\/375347","article-title":"Molecular analysis and experimental virulence of French and North American Escherichia coli neonatal meningitis isolates: identification of a new virulent clone","volume":"187","author":"S Bonacorsi","year":"2003","journal-title":"J Infect Dis"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1086\/315217","article-title":"Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise","volume":"181","author":"JR Johnson","year":"2000","journal-title":"J Infect Dis"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"3484","DOI":"10.1128\/JCM.00548-06","article-title":"Common virulence factors and genetic relationships between O18:K1:H7 Escherichia coli isolates of human and avian origin","volume":"44","author":"M Moulin-Schouleur","year":"2006","journal-title":"J Clin Microbiol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"3380","DOI":"10.1128\/AEM.02855-06","article-title":"Identification of unconventional intestinal pathogenic Escherichia coli isolates expressing intermediate virulence factor profiles by using a novel single-step multiplex PCR","volume":"73","author":"D Muller","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1553","DOI":"10.1128\/AEM.01542-06","article-title":"Autotransporter-encoding sequences are phylogenetically distributed among Escherichia coli clinical isolates and reference strains","volume":"73","author":"C Restieri","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1471-2148-13-38","article-title":"Exploring power and parameter estimation of the BiSSE method for analyzing species diversification","volume":"13","author":"MP Davis","year":"2013","journal-title":"BMC Evol Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1111\/nph.12182","article-title":"Is self-fertilization an evolutionary dead end?","volume":"198","author":"B Igic","year":"2013","journal-title":"New Phytol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"20130068","DOI":"10.1098\/rsbl.2013.0068","article-title":"Developmental mode influences diversification in ascidians","volume":"9","author":"ME Maliska","year":"2013","journal-title":"Biol Lett"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"165","DOI":"10.4137\/EBO.S39732","article-title":"Notes on the Statistical Power of the Binary State Speciation and Extinction (BiSSE) Model","volume":"12","author":"A Gamisch","year":"2016","journal-title":"Evol Bioinform Online"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1093\/biomet\/76.2.297","article-title":"Regression and time series model selection in small samples","volume":"76","author":"CM Hurvich","year":"1989","journal-title":"Biometrica"},{"key":"ref28","doi-asserted-by":"crossref","DOI":"10.3390\/pathogens5010021","article-title":"Asymtomatic Bacteriuria as a Model to Study the Coevolution of Hosts and Bacteria","volume":"5","author":"U Dobrindt","year":"2016","journal-title":"Pathogens"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"205","DOI":"10.3354\/esr003205","article-title":"Extinction of microbes: evidence and potential consequences","volume":"3","author":"MG Weinbauer","year":"2007","journal-title":"Endang Species Res"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1016\/j.ijmm.2011.09.006","article-title":"What defines extraintestinal pathogenic Escherichia coli?","volume":"301","author":"CD Kohler","year":"2011","journal-title":"Int J Med Microbiol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.jiac.2015.12.017","article-title":"Distribution of virulence associated traits among urine Escherichia coli isolates from patients in onco-hematology","volume":"22","author":"M Safi","year":"2016","journal-title":"J Infect Chemother"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.yexmp.2008.03.007","article-title":"Origins and virulence mechanisms of uropathogenic Escherichia coli","volume":"85","author":"TJ Wiles","year":"2008","journal-title":"Exp Mol Pathol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1111\/j.1574-6976.2012.00339.x","article-title":"Host-pathogen checkpoints and population bottlenecks in persistent and intracellular uropathogenic Escherichia coli bladder infection","volume":"36","author":"TJ Hannan","year":"2012","journal-title":"FEMS Microbiol Rev"},{"key":"ref34","first-page":"45","article-title":"Escherichia coli\u2014Recent Advances on Physiology, Pathogenesis and Biotechnological Applications","author":"T Kudinha","year":"2017"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/S0924-8579(02)00092-4","article-title":"Pathogenicity islands of uropathogenic E. coli and the evolution of virulence","volume":"19","author":"TA Oelschlaeger","year":"2002","journal-title":"Int J Antimicrob Agents"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005931","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,2,12]],"date-time":"2018-02-12T00:00:00Z","timestamp":1518393600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005931","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T21:42:04Z","timestamp":1588974124000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005931"}},"subtitle":[],"editor":[{"given":"Natalia L.","family":"Komarova","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,1,31]]},"references-count":35,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2018,1,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005931","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,1,31]]}}}