{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T15:57:22Z","timestamp":1792598242071,"version":"4.5.0"},"reference-count":72,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2022,6,16]],"date-time":"2022-06-16T00:00:00Z","timestamp":1655337600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,6,16]],"date-time":"2022-06-16T00:00:00Z","timestamp":1655337600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    \u2013 one of the most characterized bacteria and a major public health concern \u2013 remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient\n                    <jats:italic>E. coli<\/jats:italic>\n                    genome from a 16\n                    <jats:sup>th<\/jats:sup>\n                    century gallstone from an Italian mummy with chronic cholecystitis. We isolated ancient DNA and reconstructed the ancient\n                    <jats:italic>E. coli<\/jats:italic>\n                    genome. It consisted of one chromosome of 4446 genes and two putative plasmids with 52 genes. The\n                    <jats:italic>E. coli<\/jats:italic>\n                    strain belonged to the phylogroup A and an exceptionally rare sequence type 4995. The type VI secretion system component genes appears to be horizontally acquired from\n                    <jats:italic>Klebsiella aerogenes<\/jats:italic>\n                    , however we could not identify any pathovar specific genes nor any acquired antibiotic resistances. A sepsis mouse assay showed that a closely related contemporary\n                    <jats:italic>E. coli<\/jats:italic>\n                    strain was avirulent. Our reconstruction of this ancient\n                    <jats:italic>E. coli<\/jats:italic>\n                    helps paint a more complete picture of the burden of opportunistic infections of the past.\n                  <\/jats:p>","DOI":"10.1038\/s42003-022-03527-1","type":"journal-article","created":{"date-parts":[[2022,6,16]],"date-time":"2022-06-16T12:02:45Z","timestamp":1655380965000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["A 16th century Escherichia coli draft genome associated with an opportunistic bile infection"],"prefix":"10.1038","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9088-9848","authenticated-orcid":false,"given":"George S.","family":"Long","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Klunk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana T.","family":"Duggan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madeline","family":"Tapson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valentina","family":"Giuffra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lavinia","family":"Gazz\u00e8","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Fornaciari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2863-0907","authenticated-orcid":false,"given":"Sebastian","family":"Duchene","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gino","family":"Fornaciari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Clermont","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7860-1717","authenticated-orcid":false,"given":"Erick","family":"Denamur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G. Brian","family":"Golding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0314-4160","authenticated-orcid":false,"given":"Hendrik","family":"Poinar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,6,16]]},"reference":[{"key":"3527_CR1","doi-asserted-by":"publisher","first-page":"R1215","DOI":"10.1016\/j.cub.2020.08.081","volume":"30","author":"S Duch\u00eane","year":"2020","unstructured":"Duch\u00eane, S., Ho, S. Y., Carmichael, A. G., Holmes, E. C. & Poinar, H. The recovery, interpretation and use of ancient pathogen genomes. Curr. Biol. 30, R1215\u2013R1231 (2020).","journal-title":"Curr. Biol."},{"key":"3527_CR2","doi-asserted-by":"crossref","unstructured":"Parkins, M. D., Somayaji, R. & Waters, V. J. Epidemiology, biology, and impact of clonal Pseudomonas aeruginosa infections in cystic fibrosis. Clin. Microbiol. Rev. 31, e00019-18 (2018).","DOI":"10.1128\/CMR.00019-18"},{"key":"3527_CR3","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1128\/CMR.00092-13","volume":"27","author":"Y Achermann","year":"2014","unstructured":"Achermann, Y., Goldstein, E. J., Coenye, T. & Shirtliff, M. E. Propionibacterium acnes: from commensal to opportunistic biofilm-associated implant pathogen. Clin. Microbiol. Rev. 27, 419\u2013440 (2014).","journal-title":"Clin. Microbiol. Rev."},{"key":"3527_CR4","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1086\/204084","volume":"33","author":"JW Wood","year":"1992","unstructured":"Wood, J. W. et al. The osteological paradox: problems of inferring prehistoric health from skeletal samples. Curr. Anthropol. 33, 343\u2013370 (1992).","journal-title":"Curr. Anthropol."},{"key":"3527_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-018-03857-x","volume":"9","author":"B Krause-Kyora","year":"2018","unstructured":"Krause-Kyora, B. et al. Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans. Nat. Commun. 9, 1\u201311 (2018).","journal-title":"Nat. Commun."},{"key":"3527_CR6","doi-asserted-by":"publisher","first-page":"e1009886","DOI":"10.1371\/journal.ppat.1009886","volume":"17","author":"X Wu","year":"2021","unstructured":"Wu, X. et al. A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road. PLoS Pathog. 17, e1009886 (2021).","journal-title":"PLoS Pathog."},{"key":"3527_CR7","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1016\/S1473-3099(13)70323-2","volume":"14","author":"DM Wagner","year":"2014","unstructured":"Wagner, D. M. et al. Yersinia pestis and the Plague of Justinian 541-543 AD: a genomic analysis. Lancet Infect. Dis. 14, 319\u2013326 (2014).","journal-title":"Lancet Infect. Dis."},{"key":"3527_CR8","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nrmicro2298","volume":"8","author":"O Tenaillon","year":"2010","unstructured":"Tenaillon, O., Skurnik, D., Picard, B. & Denamur, E. The population genetics of commensal Escherichia coli. Nat. Rev. Microbiol. 8, 207\u2013217 (2010).","journal-title":"Nat. Rev. Microbiol."},{"key":"3527_CR9","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1038\/nrmicro2265","volume":"8","author":"MA Croxen","year":"2010","unstructured":"Croxen, M. A. & Finlay, B. B. Molecular mechanisms of Escherichia coli pathogenicity. Nat. Rev. Microbiol. 8, 26\u201338 (2010).","journal-title":"Nat. Rev. Microbiol."},{"key":"3527_CR10","doi-asserted-by":"publisher","first-page":"440","DOI":"10.3389\/fmicb.2018.00440","volume":"9","author":"M Rojas-Lopez","year":"2018","unstructured":"Rojas-Lopez, M., Monterio, R., Pizza, M., Desvaux, M. & Rosini, R. Intestinal pathogenic Escherichia coli: insights for vaccine development. Front. Microbiol. 9, 440 (2018).","journal-title":"Front. Microbiol."},{"key":"3527_CR11","doi-asserted-by":"crossref","unstructured":"Murray, C. J. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629\u2013655 (2022).","DOI":"10.1016\/S0140-6736(21)02724-0"},{"key":"3527_CR12","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1038\/s41579-020-0416-x","volume":"19","author":"E Denamur","year":"2021","unstructured":"Denamur, E., Clermont, O., Bonacorsi, S. & Gordon, D. The population genetics of pathogenic Escherichia coli. Nat. Rev. Microbiol. 19, 37\u201354 (2021).","journal-title":"Nat. Rev. Microbiol."},{"key":"3527_CR13","unstructured":"Fornaciari, G., Pollina, L., Tornaboni, D. & Tognetti, A. Pulmonary and hepatic pathologies in the series of mummies of s. domenico maggiore at naples (xvi century). In Proc. VII European Meeting of the Paleopathology Association (Lyon, September 1988) 89\u201392. Marino Solfanelli Editore (Journal of Paleopathology, Monographic Publications, 1989)."},{"key":"3527_CR14","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1016\/j.suc.2014.01.005","volume":"94","author":"LM Knab","year":"2014","unstructured":"Knab, L. M., Boller, A.-M. & Mahvi, D. M. Cholecystitis. Surg. Clin. North Am. 94, 455\u2013470 (2014).","journal-title":"Surg. Clin. North Am."},{"key":"3527_CR15","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1016\/j.gtc.2010.02.010","volume":"39","author":"NG Venneman","year":"2010","unstructured":"Venneman, N. G. & van Erpecum, K. J. Pathogenesis of gallstones. Gastroenterolog. Clin. North Am. 39, 171\u2013183 (2010).","journal-title":"Gastroenterolog. Clin. North Am."},{"key":"3527_CR16","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0","volume":"20","author":"DE Wood","year":"2019","unstructured":"Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 257 (2019).","journal-title":"Genome Biol."},{"key":"3527_CR17","doi-asserted-by":"crossref","unstructured":"Robertson, J. & Nash, J. H. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb. Genom. 4, e000206 (2018).","DOI":"10.1099\/mgen.0.000206"},{"key":"3527_CR18","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1101\/gr.251678.119","volume":"30","author":"Z Zhou","year":"2020","unstructured":"Zhou, Z. et al. The EnteroBase user\u2019s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res. 30, 138\u2013152 (2020).","journal-title":"Genome Res."},{"key":"3527_CR19","doi-asserted-by":"crossref","unstructured":"Rambaut, A., Lam, T. T., Carvalho, L. M. & Pybus, O. G. Pybus Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2, vew007 (2016).","DOI":"10.1093\/ve\/vew007"},{"key":"3527_CR20","doi-asserted-by":"publisher","first-page":"E2774","DOI":"10.1073\/pnas.1210309109","volume":"109","author":"H Lee","year":"2012","unstructured":"Lee, H., Popodi, E., Tang, H. & Foster, P. L. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc. Natl Acad. Sci. 109, E2774\u2013E2783 (2012).","journal-title":"Proc. Natl Acad. Sci."},{"key":"3527_CR21","doi-asserted-by":"publisher","first-page":"e1008866","DOI":"10.1371\/journal.pgen.1008866","volume":"16","author":"M Touchon","year":"2020","unstructured":"Touchon, M. et al. Phylogenetic background and habitat drive the genetic diversification of Escherichia coli. PLoS Genet. 16, e1008866 (2020).","journal-title":"PLoS Genet."},{"key":"3527_CR22","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1038\/nrmicro3185","volume":"12","author":"AB Russell","year":"2014","unstructured":"Russell, A. B., Peterson, S. B. & Mougous, J. D. Type VI secretion system effectors: poisons with a purpose. Nat. Rev. Microbiol. 12, 137\u2013148 (2014).","journal-title":"Nat. Rev. Microbiol."},{"key":"3527_CR23","doi-asserted-by":"publisher","first-page":"D687","DOI":"10.1093\/nar\/gky1080","volume":"47","author":"B Liu","year":"2019","unstructured":"Liu, B., Zheng, D., Jin, Q., Chen, L. & Yang, J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res. 47, D687\u2013D692 (2019).","journal-title":"Nucleic Acids Res."},{"key":"3527_CR24","doi-asserted-by":"publisher","first-page":"317","DOI":"10.3855\/jidc.6652","volume":"10","author":"R Morales-Espinosa","year":"2016","unstructured":"Morales-Espinosa, R. et al. UPEC strain characterization isolated from Mexican patients with recurrent urinary infections. J. Infect. Dev. Ctries. 10, 317\u2013328 (2016).","journal-title":"J. Infect. Dev. Ctries."},{"key":"3527_CR25","doi-asserted-by":"publisher","first-page":"e136","DOI":"10.1016\/j.ijid.2010.10.002","volume":"15","author":"MM Aslani","year":"2011","unstructured":"Aslani, M. M., Alikhani, M. Y., Zavari, A., Yousefi, R. & Zamani, A. R. Characterization of enteroaggregative Escherichia coli (EAEC) clinical isolates and their antibiotic resistance pattern. Int. J. Infect. Dis. 15, e136\u2013e139 (2011).","journal-title":"Int. J. Infect. Dis."},{"key":"3527_CR26","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.1086\/507305","volume":"194","author":"JR Johnson","year":"2006","unstructured":"Johnson, J. R. et al. Experimental mouse lethality of Escherichia coli isolates, in relation to accessory traits, phylogenetic group, and ecological source. J. Infect. Dis. 194, 1141\u20131150 (2006).","journal-title":"J. Infect. Dis."},{"key":"3527_CR27","first-page":"121","volume":"219","author":"JR Johnson","year":"2019","unstructured":"Johnson, J. R. et al. Accessory traits and phylogenetic background predict Escherichia coli extraintestinal virulence better than does ecological source. J. Infect. Dis. 219, 121\u2013132 (2019).","journal-title":"J. Infect. Dis."},{"key":"3527_CR28","doi-asserted-by":"publisher","first-page":"e1009065","DOI":"10.1371\/journal.pgen.1009065","volume":"16","author":"M Galardini","year":"2020","unstructured":"Galardini, M. et al. Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study. PLoS Genet. 16, e1009065 (2020).","journal-title":"PLoS Genet."},{"key":"3527_CR29","doi-asserted-by":"crossref","first-page":"D517","DOI":"10.1093\/nar\/gkz1136","volume":"48","author":"BP Alcock","year":"2020","unstructured":"Alcock, B. P. et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 48, D517\u2013D525 (2020).","journal-title":"Nucleic Acids Res."},{"key":"3527_CR30","doi-asserted-by":"crossref","unstructured":"Goldstone, R. J. & Smith, D. G. A population genomics approach to exploiting the accessory \u2019resistome\u2019 of Escherichia coli. Microb. Genom. 3, e000108 (2017).","DOI":"10.1099\/mgen.0.000108"},{"key":"3527_CR31","doi-asserted-by":"publisher","first-page":"e20983","DOI":"10.7554\/eLife.20983","volume":"6","author":"AM Devault","year":"2017","unstructured":"Devault, A. M. et al. A molecular portrait of maternal sepsis from byzantine troy. eLife 6, e20983 (2017).","journal-title":"eLife"},{"key":"3527_CR32","doi-asserted-by":"crossref","unstructured":"Friehs, K. Plasmid copy number and plasmid stability. Adv. Bioch. Eng. Biotechnol. 86, 47\u201382 (2004).","DOI":"10.1007\/b12440"},{"key":"3527_CR33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2003-4-9-r57","volume":"4","author":"V Daubin","year":"2003","unstructured":"Daubin, V., Lerat, E. & Perri\u00e8re, G. The source of laterally transferred genes in bacterial genomes. Genome Biol. 4, 1\u201312 (2003).","journal-title":"Genome Biol."},{"key":"3527_CR34","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1016\/j.meegid.2012.01.005","volume":"12","author":"RR Chaudhuri","year":"2012","unstructured":"Chaudhuri, R. R. & Henderson, I. R. The evolution of the Escherichia coli phylogeny. Infect. Genet. Evol. 12, 214\u2013226 (2012).","journal-title":"Infect. Genet. Evol."},{"key":"3527_CR35","doi-asserted-by":"crossref","unstructured":"Desroches, M. et al. The odyssey of the ancestral Escherich strain through culture collections: an example of allopatric diversification. mSphere 3, e00553-17 (2018).","DOI":"10.1128\/mSphere.00553-17"},{"key":"3527_CR36","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1111\/j.1469-0691.2009.02708.x","volume":"15","author":"M-C Wang","year":"2009","unstructured":"Wang, M.-C. et al. Different roles of host and bacterial factors in Escherichia coli extra-intestinal infections. Clin. Microbiol. Infect. 15, 372\u2013379 (2009).","journal-title":"Clin. Microbiol. Infect."},{"key":"3527_CR37","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1146\/annurev.bi.42.070173.002351","volume":"42","author":"R Benveniste","year":"1973","unstructured":"Benveniste, R. & Davies, J. Mechanisms of antibiotic resistance in bacteria. Ann. Rev. Biochem. 42, 471\u2013506 (1973).","journal-title":"Ann. Rev. Biochem."},{"key":"3527_CR38","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1038\/nrmicro1464","volume":"4","author":"LJ Piddock","year":"2006","unstructured":"Piddock, L. J. Multidrug-resistance efflux pumps? not just for resistance. Nat. Rev. Microbiol. 4, 629\u2013636 (2006).","journal-title":"Nat. Rev. Microbiol."},{"key":"3527_CR39","doi-asserted-by":"publisher","first-page":"2373","DOI":"10.1128\/jcm.27.10.2373-2375.1989","volume":"27","author":"I Brook","year":"1989","unstructured":"Brook, I. Aerobic and anaerobic microbiology of biliary tract disease. J. Clin. Microbiol. 27, 2373\u20132375 (1989).","journal-title":"J. Clin. Microbiol."},{"key":"3527_CR40","doi-asserted-by":"publisher","first-page":"3215","DOI":"10.1093\/nar\/gkp159","volume":"37","author":"C Schwarz","year":"2009","unstructured":"Schwarz, C. et al. New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains. Nucleic Acids Res. 37, 3215\u20133229 (2009).","journal-title":"Nucleic Acids Res."},{"key":"3527_CR41","doi-asserted-by":"crossref","unstructured":"Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort dna fragments. Proc. Natl Acad Sci. USA 110, 15758\u201315763 (2013).","DOI":"10.1073\/pnas.1314445110"},{"key":"3527_CR42","doi-asserted-by":"crossref","unstructured":"Glocke, I. & Meyer, M. Extending the spectrum of dna sequences retrieved from ancient bones and teeth. Genome Res. 27, 1230\u20131237 (2017).","DOI":"10.1101\/gr.219675.116"},{"key":"3527_CR43","doi-asserted-by":"publisher","DOI":"10.1186\/s13104-016-1900-2","volume":"9","author":"M Schubert","year":"2016","unstructured":"Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016).","journal-title":"BMC Res. Notes"},{"key":"3527_CR44","doi-asserted-by":"publisher","first-page":"e141","DOI":"10.1093\/nar\/gku699","volume":"42","author":"G Renaud","year":"2014","unstructured":"Renaud, G., Stenzel, U. & Kelso, J. leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res. 42, e141\u2013e141 (2014).","journal-title":"Nucleic Acids Res."},{"key":"3527_CR45","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","volume":"27","author":"R Schmieder","year":"2011","unstructured":"Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863\u2013864 (2011).","journal-title":"Bioinformatics"},{"key":"3527_CR46","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1101\/gr.213611.116","volume":"27","author":"VA Schneider","year":"2017","unstructured":"Schneider, V. A. et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res. 27, 849\u2013864 (2017).","journal-title":"Genome Res."},{"key":"3527_CR47","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"3527_CR48","doi-asserted-by":"publisher","first-page":"3407","DOI":"10.1016\/j.cub.2016.10.061","volume":"26","author":"AT Duggan","year":"2016","unstructured":"Duggan, A. T. et al. 17th century variola virus reveals the recent history of smallpox. Curr. Biol. 26, 3407\u20133412 (2016).","journal-title":"Curr. Biol."},{"key":"3527_CR49","doi-asserted-by":"publisher","first-page":"D535","DOI":"10.1093\/nar\/gkw1017","volume":"45","author":"AR Wattam","year":"2016","unstructured":"Wattam, A. R. et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res. 45, D535\u2013D542 (2016).","journal-title":"Nucleic Acids Res."},{"key":"3527_CR50","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 30, 2068\u20132069 (2014).","journal-title":"Bioinformatics"},{"key":"3527_CR51","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","volume":"31","author":"AJ Page","year":"2015","unstructured":"Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691\u20133693 (2015).","journal-title":"Bioinformatics"},{"key":"3527_CR52","doi-asserted-by":"publisher","first-page":"1682","DOI":"10.1093\/bioinformatics\/btt193","volume":"29","author":"H J\u00f3nsson","year":"2013","unstructured":"J\u00f3nsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682\u20131684 (2013).","journal-title":"Bioinformatics"},{"key":"3527_CR53","doi-asserted-by":"publisher","first-page":"102383","DOI":"10.1016\/j.isci.2021.102383","volume":"24","author":"A Seguin-Orlando","year":"2021","unstructured":"Seguin-Orlando, A. et al. No particular genomic features underpin the dramatic economic consequences of 17th century plague epidemics in italy. iScience 24, 102383 (2021).","journal-title":"iScience"},{"key":"3527_CR54","doi-asserted-by":"crossref","unstructured":"Nurk, S. et al. Assembling genomes and mini-metagenomes from highly chimeric reads. In Annual International Conference on Research in Computational Molecular Biology (Springer, 2013).","DOI":"10.1007\/978-3-642-37195-0_13"},{"key":"3527_CR55","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gku1196","volume":"43","author":"NJ Croucher","year":"2015","unstructured":"Croucher, N. J. et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using gubbins. Nucleic Acids Res. 43, e15\u2013e15 (2015).","journal-title":"Nucleic Acids Res."},{"key":"3527_CR56","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530\u20131534 (2020).","journal-title":"Mol. Biol. Evol."},{"key":"3527_CR57","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","volume":"14","author":"S Kalyaanamoorthy","year":"2017","unstructured":"Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K., Von Haeseler, A. & Jermiin, L. S. Modelfinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587\u2013589 (2017).","journal-title":"Nat. Methods"},{"key":"3527_CR58","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-018-2164-8","volume":"19","author":"F Menardo","year":"2018","unstructured":"Menardo, F. et al. Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC Bioinformatics 19, 1\u20138 (2018).","journal-title":"BMC Bioinformatics"},{"key":"3527_CR59","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. 4, e000192 (2018).","DOI":"10.1099\/mgen.0.000192"},{"key":"3527_CR60","doi-asserted-by":"crossref","unstructured":"Hazen, T. H. et al. Investigating the relatedness of enteroinvasive Escherichia coli to other E. coli and Shigella isolates by using comparative genomics. Infect. Immun. 84, 2362\u20132371 (2016).","DOI":"10.1128\/IAI.00350-16"},{"key":"3527_CR61","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1111\/1758-2229.12019","volume":"5","author":"O Clermont","year":"2013","unstructured":"Clermont, O., Christenson, J. K., Denamur, E. & Gordon, D. M. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ. Microbiol. Rep. 5, 58\u201365 (2013).","journal-title":"Environ. Microbiol. Rep."},{"key":"3527_CR62","doi-asserted-by":"publisher","first-page":"1321","DOI":"10.1038\/ng.3145","volume":"46","author":"A von Mentzer","year":"2014","unstructured":"von Mentzer, A. et al. Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution. Nat. Genet. 46, 1321 (2014).","journal-title":"Nat. Genet."},{"key":"3527_CR63","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1093\/sysbio\/syv068","volume":"65","author":"T-H To","year":"2016","unstructured":"To, T.-H., Jung, M., Lycett, S. & Gascuel, O. Fast dating using least-squares criteria and algorithms. Syst. Biol. 65, 82\u201397 (2016).","journal-title":"Syst. Biol."},{"key":"3527_CR64","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12862-018-1210-5","volume":"18","author":"S Duchene","year":"2018","unstructured":"Duchene, S. et al. Inferring demographic parameters in bacterial genomic data using bayesian and hybrid phylogenetic methods. BMC Evol. Biol. 18, 1\u201311 (2018).","journal-title":"BMC Evol. Biol."},{"key":"3527_CR65","doi-asserted-by":"publisher","first-page":"vey016","DOI":"10.1093\/ve\/vey016","volume":"4","author":"MA Suchard","year":"2018","unstructured":"Suchard, M. A. et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4, vey016 (2018).","journal-title":"Virus Evol."},{"key":"3527_CR66","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1073\/pnas.98.2.525","volume":"98","author":"MM Riehle","year":"2001","unstructured":"Riehle, M. M., Bennett, A. F. & Long, A. D. Genetic architecture of thermal adaptation in Escherichia coli. Proc. Natl Acad. Sci. USA 98, 525\u2013530 (2001).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"3527_CR67","doi-asserted-by":"publisher","first-page":"D607","DOI":"10.1093\/nar\/gky1131","volume":"47","author":"D Szklarczyk","year":"2019","unstructured":"Szklarczyk, D. et al. STRING v11: protein\u2013protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607\u2013D613 (2019).","journal-title":"Nucleic Acids Res."},{"key":"3527_CR68","doi-asserted-by":"publisher","first-page":"2334","DOI":"10.1093\/jac\/dkaa161","volume":"75","author":"V de Lastours","year":"2020","unstructured":"de Lastours, V. et al. Mortality in Escherichia coli bloodstream infections: antibiotic resistance still does not make it. J. Antimicrob. Chemother. 75, 2334\u20132343 (2020).","journal-title":"J. Antimicrob. Chemother."},{"key":"3527_CR69","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).","journal-title":"BMC Bioinformatics"},{"key":"3527_CR70","doi-asserted-by":"publisher","first-page":"e1000344","DOI":"10.1371\/journal.pgen.1000344","volume":"5","author":"M Touchon","year":"2009","unstructured":"Touchon, M. et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5, e1000344 (2009).","journal-title":"PLoS Genet."},{"key":"3527_CR71","doi-asserted-by":"publisher","unstructured":"longg2. longg2\/AncientEcoli: published version. Zenodo https:\/\/doi.org\/10.5281\/zenodo.6403348 (2022).","DOI":"10.5281\/zenodo.6403348"},{"key":"3527_CR72","doi-asserted-by":"publisher","unstructured":"longg2. longg2\/LongBioinformatics: ancient Ecoli version. Zenodo https:\/\/doi.org\/10.5281\/zenodo.6403351 (2022).","DOI":"10.5281\/zenodo.6403351"}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-022-03527-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-022-03527-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-022-03527-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,25]],"date-time":"2022-11-25T03:47:23Z","timestamp":1669348043000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-022-03527-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,16]]},"references-count":72,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,12]]}},"alternative-id":["3527"],"URL":"https:\/\/doi.org\/10.1038\/s42003-022-03527-1","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-1409634\/v1","asserted-by":"object"}]},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,16]]},"assertion":[{"value":"1 March 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 May 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 June 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"599"}}