Evidence for Neolithic acquisition of the high pathogenic island by Escherichia coli followed by recent selection

Evidence for Neolithic acquisition of the high pathogenic island by Escherichia coli followed by recent selection | bioRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return"[object Function]"==o.call(a)}function e(a){return"string"==typeof a}function f(){}function g(a){return!a||"loaded"==a||"complete"==a||"uninitialized"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){("c"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){"img"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),"object"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height="0",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),"img"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||"j",e(a)?i("c"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName("script")[0],o={}.toString,p=[],q=0,r="MozAppearance"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&"[object Opera]"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?"object":l?"script":"img",v=l?"script":u,w=Array.isArray||function(a){return"[object Array]"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split("!"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split("="),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(".").pop().split("?").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split("/").pop().split("?")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&"css"==i.url.split(".").pop().split("?").shift()?"c":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-M677548'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results Evidence for Neolithic acquisition of the high pathogenic island by Escherichia coli followed by recent selection View ORCID Profile Julie Marin , View ORCID Profile Erick Denamur , View ORCID Profile Olivier Tenaillon , Francois Blanquart doi: https://doi.org/10.1101/2025.09.17.676721 Julie Marin 1 Sorbonne Paris Nord; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Julie Marin For correspondence: julie.marin{at}univ-paris13.fr Erick Denamur 2 INSERM; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Erick Denamur Olivier Tenaillon 3 Inserm; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Olivier Tenaillon Francois Blanquart 4 CNRS Find this author on Google Scholar Find this author on PubMed Search for this author on this site Abstract Info/History Metrics Supplementary material Preview PDF Abstract Many genetic elements involved in virulence and pathogenicity have been identified in commensal bacteria that are also opportunistic pathogens, but how these elements evolve is less well known. Understanding the evolutionary history of virulence elements requires genomes sampled in commensalism in healthy hosts, as genomes from bacterial infections are biased towards higher pathogenicity. Here, using a rare collection of human commensal Escherichia coli sampled in France from 1980 to 2020, we inferred the evolutionary history of the High Pathogenicity Island (HPI), a key virulence factor of E. coli with an uncertain evolutionary origin. The most likely scenario implied a horizontal transfer of the HPI from Yersinia pestis/pseudotuberculosis to the Enterobacterales, including E. coli, ~4,700 years ago, coinciding with a period of high prevalence of the plague in the Neolithic. The element subsequently spread in E. coli, with signs of positive epistasis with phylogroups B2 and F, and was positively selected in the last 100 years. Our work sheds light on the history and mode of evolution of virulence in an important opportunistic pathogen. It suggests the Neolithic period may have favored not only the emergence of zoonotic pathogens but also gene transfer between bacterial species, enriching the gene repertoire of major pathogens with potentially important implications on public health nowadays. Competing Interest Statement The authors have declared no competing interest. Footnotes To further assess the robustness of our conclusions, we explicitly analysed alternative, non-supported rooting scenarios which would result in the opposite transfer, E. coli -> Y. pestis or K. pneumoniae -> Y. pestis. These alternative scenarios (not backed up by molecular evidence) lead to an implausible inferred date of transfer to Y. pestis, at 56,612 years ago, while the emergence of the species is dated 5,700-6,000 years ago. Moreover, these scenarios resulted in molecular rates ~100-fold slower than what is known from the literature. On the contrary, our proposed scenario with a transfer of the HPI from Y. pestis to the Enterobacterales leads to consistent rates of evolution and consistent dating of evolutionary events concerning Y. pestis. Funder Information Declared CNRS , Momemtum Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . View the discussion thread. Back to top Previous Next Posted May 23, 2026. Download PDF Supplementary Material Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. 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Share Evidence for Neolithic acquisition of the high pathogenic island by Escherichia coli followed by recent selection Julie Marin , Erick Denamur , Olivier Tenaillon , Francois Blanquart bioRxiv 2025.09.17.676721; doi: https://doi.org/10.1101/2025.09.17.676721 Share This Article: Copy Citation Tools Evidence for Neolithic acquisition of the high pathogenic island by Escherichia coli followed by recent selection Julie Marin , Erick Denamur , Olivier Tenaillon , Francois Blanquart bioRxiv 2025.09.17.676721; doi: https://doi.org/10.1101/2025.09.17.676721 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Evolutionary Biology Subject Areas All Articles Animal Behavior and Cognition (7635) Biochemistry (17691) Bioengineering (13892) Bioinformatics (41937) Biophysics (21452) Cancer Biology (18588) Cell Biology (25504) Clinical Trials (138) Developmental Biology (13378) Ecology (19899) Epidemiology (2067) Evolutionary Biology (24320) Genetics (15609) Genomics (22506) Immunology (17736) Microbiology (40394) Molecular Biology (17181) Neuroscience (88605) Paleontology (666) Pathology (2832) Pharmacology and Toxicology (4824) Physiology (7641) Plant Biology (15156) Scientific Communication and Education (2045) Synthetic Biology (4294) Systems Biology (9825) Zoology (2271)