{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T21:50:00Z","timestamp":1768513800867,"version":"3.49.0"},"posted":{"date-parts":[[2024,6,17]]},"group-title":"Immunology","reference-count":56,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2024,6,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The\n                  <jats:italic>E. coli<\/jats:italic>\n                  strain harboring the polyketide synthase\n                  <jats:bold>(<\/jats:bold>\n                  <jats:italic>Pks)<\/jats:italic>\n                  island encodes the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involved whole-genome-wide comparison and phylogenetic analysis of\n                  <jats:italic>pks<\/jats:italic>\n                  harboring\n                  <jats:italic>E. coli<\/jats:italic>\n                  isolates to gain insight into the distribution and evolution of these organism. Fifteen\n                  <jats:italic>E. coli<\/jats:italic>\n                  strains isolated from patients with ulcerative colitis were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for\n                  <jats:italic>pks<\/jats:italic>\n                  harboring\n                  <jats:italic>E. coli<\/jats:italic>\n                  genomes, 158 of which were\n                  <jats:italic>pks<\/jats:italic>\n                  -positive isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158+13)\n                  <jats:italic>pks<\/jats:italic>\n                  -positive isolates belonged to phylogroup B2, and most of the isolates associated to sequence types ST73 and ST95. One isolate from an ulcerative colitis (UC) patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of\n                  <jats:italic>pks<\/jats:italic>\n                  -positive isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the preponderance of virulence genes and a reduced number of antimicrobial genes in\n                  <jats:italic>Pks<\/jats:italic>\n                  -positive isolates. This study strongly contributes to understanding the evolution of\n                  <jats:italic>pks<\/jats:italic>\n                  islands in\n                  <jats:italic>E. coli<\/jats:italic>\n                  .\n                <\/jats:p>","DOI":"10.1101\/2024.06.16.599199","type":"posted-content","created":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T00:10:26Z","timestamp":1718669426000},"source":"Crossref","is-referenced-by-count":1,"title":["Genomic characterization of\n                  <i>Escherichia coli<\/i>\n                  harbor a polyketide synthase (\n                  <i>pks<\/i>\n                  ) island associated with colorectal cancer (CRC) development"],"prefix":"10.64898","author":[{"given":"Chao","family":"Lv","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohd","family":"Abdullah","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weiye","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nan","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zile","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yiwen","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Min","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenneth W.","family":"Simpson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ahmed","family":"Elsaadi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongzhang","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven M.","family":"Lipkin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yung-Fu","family":"Chang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2024062207500489000_2024.06.16.599199v1.1","doi-asserted-by":"crossref","unstructured":"Pakbin B , Bruck WM , Rossen JWA: Virulence Factors of Enteric Pathogenic Escherichia coli: A Review. Int J Mol Sci 2021, 22.","DOI":"10.20944\/preprints202108.0348.v1"},{"key":"2024062207500489000_2024.06.16.599199v1.2","doi-asserted-by":"crossref","first-page":"3","DOI":"10.30802\/AALAS-CM-20-000054","article-title":"Fox JG: A One Health Perspective for Defining and Deciphering Escherichia coli Pathogenic Potential in Multiple Hosts","volume":"71","year":"2021","journal-title":"Comp Med"},{"key":"2024062207500489000_2024.06.16.599199v1.3","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1002\/ijc.21453","article-title":"Aberrant promoter methylation of multiple genes during multistep pathogenesis of colorectal cancers","volume":"118","year":"2006","journal-title":"International journal of cancer Journal international du cancer"},{"key":"2024062207500489000_2024.06.16.599199v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2298"},{"key":"2024062207500489000_2024.06.16.599199v1.5","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00740-12"},{"key":"2024062207500489000_2024.06.16.599199v1.6","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-020-0416-x"},{"key":"2024062207500489000_2024.06.16.599199v1.7","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.10.4555-4558.2000"},{"key":"2024062207500489000_2024.06.16.599199v1.8","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1889"},{"key":"2024062207500489000_2024.06.16.599199v1.9","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.54.1.641"},{"key":"2024062207500489000_2024.06.16.599199v1.10","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro884"},{"key":"2024062207500489000_2024.06.16.599199v1.11","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)81985-6"},{"key":"2024062207500489000_2024.06.16.599199v1.12","doi-asserted-by":"crossref","unstructured":"Fais T , Delmas J , Barnich N , Bonnet R , Dalmasso G: Colibactin: More Than a New Bacterial Toxin. Toxins (Basel) 2018, 10.","DOI":"10.3390\/toxins10040151"},{"key":"2024062207500489000_2024.06.16.599199v1.13","doi-asserted-by":"publisher","DOI":"10.1126\/science.1127059"},{"key":"2024062207500489000_2024.06.16.599199v1.14","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1001261107"},{"key":"2024062207500489000_2024.06.16.599199v1.15","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00716-15"},{"key":"2024062207500489000_2024.06.16.599199v1.16","doi-asserted-by":"publisher","DOI":"10.1126\/science.1224820"},{"key":"2024062207500489000_2024.06.16.599199v1.17","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2013-305257"},{"key":"2024062207500489000_2024.06.16.599199v1.18","doi-asserted-by":"crossref","unstructured":"Nouri R , Hasani A , Masnadi Shirazi K , Alivand MR , Sepehri B , Sotoudeh S , Hemmati F , Fattahzadeh A , Abdinia B , Ahangarzadeh Rezaee M : Mucosa-Associated Escherichia coli in Colorectal Cancer Patients and Control Subjects: Variations in the Prevalence and Attributing Features. Can J Infect Dis Med Microbiol 2021, 2021:2131787.","DOI":"10.1155\/2021\/2131787"},{"key":"2024062207500489000_2024.06.16.599199v1.19","doi-asserted-by":"crossref","unstructured":"Wernke KM , Xue M , Tirla A , Kim CS , Crawford JM , Herzon SB: Structure and bioactivity of colibactin. Bioorg Med Chem Lett 2020, 30:127280.","DOI":"10.1016\/j.bmcl.2020.127280"},{"key":"2024062207500489000_2024.06.16.599199v1.20","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1038\/s41467-021-21162-y","article-title":"Meyer TF: Genomic aberrations after short-term exposure to colibactin-producing E. coli transform primary colon epithelial cells","volume":"12","year":"2021","journal-title":"Nat Commun"},{"key":"2024062207500489000_2024.06.16.599199v1.21","unstructured":"Dejea CM , Fathi P , Craig JA-O , Boleij AA-O , Taddese RA-O , Geis AA-O , Wu XA-OX , DeStefano Shields CA-O , Hechenbleikner EA-O , Huso DL , et al: Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria."},{"key":"2024062207500489000_2024.06.16.599199v1.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2020.12.001"},{"key":"2024062207500489000_2024.06.16.599199v1.23","unstructured":"Arthur JC , Perez-Chanona E Fau - M\u00fchlbauer M , M\u00fchlbauer M Fau - Tomkovich S , Tomkovich S Fau - Uronis JM , Uronis Jm Fau - Fan T-J , Fan Tj Fau - Campbell BJ , Campbell Bj Fau - Abujamel T , Abujamel T Fau - Dogan B , Dogan B Fau - Rogers AB , Rogers Ab Fau - Rhodes JM , et al: Intestinal inflammation targets cancer-inducing activity of the microbiota."},{"key":"2024062207500489000_2024.06.16.599199v1.24","unstructured":"Cougnoux A , Dalmasso G , Martinez R , Buc E , Delmas J , Gibold L , Sauvanet P , Darcha C , D\u00e9chelotte P , Bonnet M , et al: Bacterial genotoxin colibactin promotes colon tumor growth by inducing a senescence-associated secretory phenotype."},{"key":"2024062207500489000_2024.06.16.599199v1.25","unstructured":"Dziuba\u0144ska-Kusibab PJ , Berger HA-O , Battistini F , Bouwman BA-O , Iftekhar A , Katainen R , Cajuso T , Crosetto N , Orozco M , Aaltonen LA, Meyer TA-O: Colibactin DNA-damage signature indicates mutational impact in colorectal cancer."},{"key":"2024062207500489000_2024.06.16.599199v1.26","unstructured":"Pleguezuelos-Manzano C , Puschhof J , Rosendahl Huber A , van Hoeck AA-O , Wood HA-O , Nomburg J , Gurjao C , Manders FA-OX , Dalmasso GA-OX , Stege PB, et al: Mutational signature in colorectal cancer caused by genotoxic pks(+) E. coli."},{"key":"2024062207500489000_2024.06.16.599199v1.27","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1008029"},{"key":"2024062207500489000_2024.06.16.599199v1.28","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00522-09"},{"key":"2024062207500489000_2024.06.16.599199v1.29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0056964"},{"key":"2024062207500489000_2024.06.16.599199v1.30","doi-asserted-by":"publisher","DOI":"10.1126\/science.aah3648"},{"key":"2024062207500489000_2024.06.16.599199v1.31","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiu071"},{"key":"2024062207500489000_2024.06.16.599199v1.32","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00064-15"},{"key":"2024062207500489000_2024.06.16.599199v1.33","doi-asserted-by":"crossref","unstructured":"Lu MC , Chen YT , Chiang MK , Wang YC , Hsiao PY , Huang YJ , Lin CT , Cheng CC , Liang CL , Lai YC: Colibactin Contributes to the Hypervirulence of pks(+) K1 CC23 Klebsiella pneumoniae in Mouse Meningitis Infections. Front Cell Infect Microbiol 2017, 7:103.","DOI":"10.3389\/fcimb.2017.00103"},{"key":"2024062207500489000_2024.06.16.599199v1.34","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2004.03.054"},{"key":"2024062207500489000_2024.06.16.599199v1.35","doi-asserted-by":"crossref","unstructured":"Liu H XB , Zheng J , Zhong H , Yu Y , Peng D , Sun M .: Build a bioinformatics analysis platform and apply it to routine analysis of microbial genomics and comparative genomics. Protocol exchange 2022.","DOI":"10.21203\/rs.2.21224\/v6"},{"key":"2024062207500489000_2024.06.16.599199v1.36","doi-asserted-by":"crossref","unstructured":"Beghain J , Bridier-Nahmias A , Le Nagard H , Denamur E , Clermont O: ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microb Genom 2018, 4.","DOI":"10.1099\/mgen.0.000192"},{"key":"2024062207500489000_2024.06.16.599199v1.37","doi-asserted-by":"crossref","unstructured":"Jolley KA , Maiden MC: BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010, 11:595.","DOI":"10.1186\/1471-2105-11-595"},{"key":"2024062207500489000_2024.06.16.599199v1.38","doi-asserted-by":"crossref","unstructured":"Bessonov K , Laing C , Robertson J , Yong I , Ziebell K , Gannon VPJ , Nichani A , Arya G , Nash JHE , Christianson S: ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data. Microb Genom 2021, 7.","DOI":"10.1099\/mgen.0.000728"},{"key":"2024062207500489000_2024.06.16.599199v1.39","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw582"},{"key":"2024062207500489000_2024.06.16.599199v1.40","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"2024062207500489000_2024.06.16.599199v1.41","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"2024062207500489000_2024.06.16.599199v1.42","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009490"},{"key":"2024062207500489000_2024.06.16.599199v1.43","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky783"},{"key":"2024062207500489000_2024.06.16.599199v1.44","doi-asserted-by":"crossref","unstructured":"Jia B , Raphenya AR , Alcock B , Waglechner N , Guo P , Tsang KK , Lago BA , Dave BM , Pereira S , Sharma AN , et al: CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 2017, 45:D566\u2013D573.","DOI":"10.1093\/nar\/gkw1004"},{"key":"2024062207500489000_2024.06.16.599199v1.45","doi-asserted-by":"crossref","unstructured":"Chen L , Zheng D , Liu B , Yang J , Jin Q : VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on. Nucleic Acids Res 2016, 44:D694\u2013697.","DOI":"10.1093\/nar\/gkv1239"},{"key":"2024062207500489000_2024.06.16.599199v1.46","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw387"},{"key":"2024062207500489000_2024.06.16.599199v1.47","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr485"},{"key":"2024062207500489000_2024.06.16.599199v1.48","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp030"},{"key":"2024062207500489000_2024.06.16.599199v1.49","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr039"},{"key":"2024062207500489000_2024.06.16.599199v1.50","doi-asserted-by":"crossref","unstructured":"Chagneau CV , Garcie C , Bossuet-Greif N , Tronnet S , Brachmann AO , Piel J , Nougayrede JP , Martin P , Oswald E: The Polyamine Spermidine Modulates the Production of the Bacterial Genotoxin Colibactin. mSphere 2019, 4.","DOI":"10.1128\/mSphere.00414-19"},{"key":"2024062207500489000_2024.06.16.599199v1.51","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2017.10.009"},{"key":"2024062207500489000_2024.06.16.599199v1.52","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00949-08"},{"key":"2024062207500489000_2024.06.16.599199v1.53","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02365-09"},{"key":"2024062207500489000_2024.06.16.599199v1.54","doi-asserted-by":"crossref","unstructured":"Auvray F , Perrat A , Arimizu Y , Chagneau CV , Bossuet-Greif N , Massip C , Brugere H , Nougayrede JP , Hayashi T , Branchu P , et al: Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population. Microb Genom 2021, 7.","DOI":"10.1099\/mgen.0.000579"},{"key":"2024062207500489000_2024.06.16.599199v1.55","doi-asserted-by":"crossref","unstructured":"Suresh A , Ranjan A , Jadhav S , Hussain A , Shaik S , Alam M , Baddam R , Wieler LH , Ahmed N: Molecular Genetic and Functional Analysis of pks-Harboring, Extra-Intestinal Pathogenic Escherichia coli From India. Front Microbiol 2018, 9:2631.","DOI":"10.3389\/fmicb.2018.02631"},{"key":"2024062207500489000_2024.06.16.599199v1.56","doi-asserted-by":"crossref","unstructured":"Suresh A , Shaik S , Baddam R , Ranjan A , Qumar S , Jadhav S , Semmler T , Ghazi IA , Wieler LH , Ahmed N: Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island. mBio 2021, 12.","DOI":"10.1128\/mBio.03634-20"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2024.06.16.599199","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T06:35:20Z","timestamp":1768458920000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2024.06.16.599199"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,17]]},"references-count":56,"URL":"https:\/\/doi.org\/10.1101\/2024.06.16.599199","relation":{},"subject":[],"published":{"date-parts":[[2024,6,17]]},"subtype":"preprint"}}