{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:49:39Z","timestamp":1787010579619,"version":"build-2736575974"},"reference-count":46,"publisher":"Microbiology Society","issue":"4","license":[{"start":{"date-parts":[[2020,4,1]],"date-time":"2020-04-01T00:00:00Z","timestamp":1585699200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/L01680X\/1"],"award-info":[{"award-number":["BB\/L01680X\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/J004227\/1"],"award-info":[{"award-number":["BB\/J004227\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/J004227\/1"],"award-info":[{"award-number":["BB\/J004227\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/J004227\/1"],"award-info":[{"award-number":["BB\/J004227\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/P013740\/1"],"award-info":[{"award-number":["BB\/P013740\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/P013740\/1"],"award-info":[{"award-number":["BB\/P013740\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/P013740\/1"],"award-info":[{"award-number":["BB\/P013740\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:p>\n                    <jats:italic>\n                      <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.3514\" xlink:type=\"simple\">Lawsonia intracellularis<\/jats:ext-link>\n                      <\/jats:named-content>\n                    <\/jats:italic>\n                    is a Gram-negative obligate intracellular bacterium that is the aetiological agent of proliferative enteropathy (PE), a common intestinal disease of major economic importance in pigs and other animal species. To date, progress in understanding the biology of\n                    <jats:italic>\n                      <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.3514\" xlink:type=\"simple\">L. intracellularis<\/jats:ext-link>\n                      <\/jats:named-content>\n                    <\/jats:italic>\n                    for improved disease control has been hampered by the inability to culture the organism\n                    <jats:italic>in vitro<\/jats:italic>\n                    . In particular, our understanding of the genomic diversity and population structure of clinical\n                    <jats:italic>L. intercellularis<\/jats:italic>\n                    is very limited. Here, we utilized a metagenomic shotgun approach to directly sequence and assemble 21\n                    <jats:italic>\n                      <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.3514\" xlink:type=\"simple\">L<\/jats:ext-link>\n                      <\/jats:named-content>\n                    <\/jats:italic>\n                    .\n                    <jats:italic>\n                      <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.3514\" xlink:type=\"simple\">intracellularis<\/jats:ext-link>\n                      <\/jats:named-content>\n                    <\/jats:italic>\n                    genomes from faecal and ileum samples of infected pigs and horses across three continents. Phylogenetic analysis revealed a genetically monomorphic clonal lineage responsible for infections in pigs, with distinct subtypes associated with infections in horses. The genome was highly conserved, with 94\u200a% of genes shared by all isolates and a very small accessory genome made up of only 84 genes across all sequenced strains. In part, the accessory genome was represented by regions with a high density of SNPs, indicative of recombination events importing novel gene alleles. In summary, our analysis provides the first view of the population structure for\n                    <jats:italic>\n                      <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.3514\" xlink:type=\"simple\">L. intracellularis<\/jats:ext-link>\n                      <\/jats:named-content>\n                    <\/jats:italic>\n                    , revealing a single major lineage associated with disease of pigs. The limited diversity and broad geographical distribution suggest the recent emergence and clonal expansion of an important livestock pathogen.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.000358","type":"journal-article","created":{"date-parts":[[2020,4,2]],"date-time":"2020-04-02T12:17:57Z","timestamp":1585829877000},"source":"Crossref","is-referenced-by-count":5,"title":["Metagenomic sequencing of clinical samples reveals a single widespread clone of Lawsonia intracellularis responsible for porcine proliferative enteropathy"],"prefix":"10.1099","volume":"6","author":[{"given":"Rebecca J.","family":"Bengtsson","sequence":"first","affiliation":[{"name":"Institute of Integrative Biology, University of Liverpool, Liverpool, UK"},{"name":"Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan A.","family":"Wee","sequence":"additional","affiliation":[{"name":"Usher Institute, University of Edinburgh, Edinburgh, UK"},{"name":"Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gonzalo","family":"Yebra","sequence":"additional","affiliation":[{"name":"Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rodrigo","family":"Bacigalupe","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Biology, Rega Institute for Medical Research, KU Leuven, Belgium"},{"name":"Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleanor","family":"Watson","sequence":"additional","affiliation":[{"name":"Moredun Research Institute, Penicuik, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberto M. C.","family":"Guedes","sequence":"additional","affiliation":[{"name":"Veterinary School, Department of Clinic and Surgery, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magdalena","family":"Jacobson","sequence":"additional","affiliation":[{"name":"Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8889-8120","authenticated-orcid":false,"given":"Tomasz","family":"Stadejek","sequence":"additional","affiliation":[{"name":"ANSES Foug\u00e8res Laboratory, 10B rue Claude Bourgelat, Javen\u00e9 CS 40608, BP 90203, 35306 FOUG\u00c8RES, France"},{"name":"Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9213-1830","authenticated-orcid":false,"given":"Alan L.","family":"Archibald","sequence":"additional","affiliation":[{"name":"Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Ross","family":"Fitzgerald","sequence":"additional","affiliation":[{"name":"Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tahar","family":"Ait-Ali","sequence":"additional","affiliation":[{"name":"Department of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","first-page":"533","article-title":"Ileal symbiont intracellularis, an obligate intracellular bacterium of porcine intestines showing a relationship to Desulfovibrio species","volume":"43","author":"Gebhart","year":"1993","journal-title":"International Journal of Systematic and Evolutionary Microbiology"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600-0684.1999.tb00084.x"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1053\/jcpa.1999.0347"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.7589\/0090-3558-44.4.992"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcpa.2008.03.001"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1136\/vr.91.10.235"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcpa.2010.03.005"},{"key":"R8","first-page":"565","article-title":"Lawsonia intracellularis-associated proliferative enteritis in weanling foals in the Netherlands","volume":"136","author":"Van Den Wollenberg","year":"2011","journal-title":"Tijdschr Diergeneeskd"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1111\/evj.12075"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.2746\/095777309X453119"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.2746\/042516400777591110"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1111\/j.1939-1676.2010.0482.x"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1186\/1297-9716-43-53"},{"key":"R14","first-page":"261","article-title":"Species-Specificity of equine and porcine Lawsonia intracellularis isolates in laboratory animals","volume":"77","author":"Sampieri","year":"2013","journal-title":"Canadian Journal of Veterinary Research"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.31.5.1136-1142.1993"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.05976-11"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.00027-13"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2004.04.014"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-3-r46"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv033"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.1165"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1101\/gr.186072.114"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt086"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"R29","article-title":"snippy: fast bacterial variant calling from NGS reads","author":"Seemann","year":"2015"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv566"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0524-x"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr703"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx610"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msu300"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4285"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1101\/gr.213959.116"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1128\/MRA.01021-18"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1186\/1297-9716-44-49"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-14-421"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1872"},{"key":"R42","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1472"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2006.01.004"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-26036-w"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.1136\/vr.149.24.729"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2018.00031"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000358?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T21:23:48Z","timestamp":1702589028000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000358"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,4,1]]},"references-count":46,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2020,4,1]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.000358","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,1]]}}}