{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T22:28:58Z","timestamp":1771540138646,"version":"3.50.1"},"reference-count":58,"publisher":"Wiley","issue":"12","license":[{"start":{"date-parts":[[2020,6,23]],"date-time":"2020-06-23T00:00:00Z","timestamp":1592870400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/N002903\/1"],"award-info":[{"award-number":["BB\/N002903\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/P504737\/1"],"award-info":[{"award-number":["BB\/P504737\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["104169\/Z\/14\/Z"],"award-info":[{"award-number":["104169\/Z\/14\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["enviromicro-journals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Environmental Microbiology"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Summary<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Listeria monocytogenes<\/jats:italic>\n                    is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracking of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage\u2010specific characteristics call for a more detailed understanding of evolution. In our work, we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of\n                    <jats:italic>L<\/jats:italic>\n                    .\n                    <jats:italic>monocytogenes<\/jats:italic>\n                    we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub\u2010lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage\u2010mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub\u2010lineages and lineages, we found that the previously proposed cut\u2010off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of\n                    <jats:italic>L<\/jats:italic>\n                    .\n                    <jats:italic>monocytogenes<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.1111\/1462-2920.15111","type":"journal-article","created":{"date-parts":[[2020,6,2]],"date-time":"2020-06-02T02:04:45Z","timestamp":1591063485000},"page":"5058-5072","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Lineage\u2010specific evolution and gene flow in\n                    <scp>\n                      <i>Listeria monocytogenes<\/i>\n                    <\/scp>\n                    are independent of bacteriophages"],"prefix":"10.1111","volume":"22","author":[{"given":"Roxana","family":"Zamudio","sequence":"first","affiliation":[{"name":"Department of Genetics and Genome Biology University of Leicester  Leicester UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard D.","family":"Haigh","sequence":"additional","affiliation":[{"name":"Department of Respiratory Sciences University of Leicester  Leicester UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph D.","family":"Ralph","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genome Biology University of Leicester  Leicester UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Megan","family":"De Ste Croix","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genome Biology University of Leicester  Leicester UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taurai","family":"Tasara","sequence":"additional","affiliation":[{"name":"Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich  Zurich Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katrin","family":"Zurfluh","sequence":"additional","affiliation":[{"name":"Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich  Zurich Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Min Jung","family":"Kwun","sequence":"additional","affiliation":[{"name":"MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology Imperial College London  London UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew D.","family":"Millard","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genome Biology University of Leicester  Leicester UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephen D.","family":"Bentley","sequence":"additional","affiliation":[{"name":"Parasites and Microbes Wellcome Trust Sanger Institute  Hinxton UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas J.","family":"Croucher","sequence":"additional","affiliation":[{"name":"MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology Imperial College London  London UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roger","family":"Stephan","sequence":"additional","affiliation":[{"name":"Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich  Zurich Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4117-793X","authenticated-orcid":false,"given":"Marco R.","family":"Oggioni","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genome Biology University of Leicester  Leicester UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2020,6,23]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2014.1747"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw387"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.182.20.5931-5934.2000"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.yrtph.2005.08.005"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1164783"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aat5867"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02091-16"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01532-16"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fux025"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2148-8-277"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00720-14"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01041-09"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.3390\/v10080397"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.foodcont.2015.04.030"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-5-113"},{"key":"e_1_2_7_20_1","first-page":"5500","article-title":"The European Union summary report on trends and sources of zoonoses, zoonotic agents and food\u2010borne outbreaks in 2016","volume":"16","author":"EFSA and ECDC","year":"2017","journal-title":"EFSA J"},{"key":"e_1_2_7_21_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.7973728"},{"key":"e_1_2_7_22_1","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.12342"},{"key":"e_1_2_7_23_1","doi-asserted-by":"crossref","first-page":"20469","DOI":"10.2807\/ese.18.18.20469-en","article-title":"Outbreak of Listerosis due to imported cooked ham, Switzerland 2011","volume":"18","author":"H\u00e4chler H.","year":"2013","journal-title":"Eurosurveillance"},{"key":"e_1_2_7_24_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2014.00159"},{"key":"e_1_2_7_25_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00119-18"},{"key":"e_1_2_7_26_1","first-page":"453142","article-title":"SKA: Split kmer analysis toolkit for bacterial genomic epidemiology","author":"Harris S.R.","year":"2018","journal-title":"BioRxiv"},{"key":"e_1_2_7_27_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2000.01643.x"},{"key":"e_1_2_7_28_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-595"},{"key":"e_1_2_7_29_1","doi-asserted-by":"publisher","DOI":"10.4161\/bact.26861"},{"key":"e_1_2_7_30_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2016.12.008"},{"key":"e_1_2_7_31_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-14-47"},{"key":"e_1_2_7_32_1","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens7020052"},{"key":"e_1_2_7_33_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002453"},{"key":"e_1_2_7_34_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.241455.118"},{"key":"e_1_2_7_35_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2000.01720.x"},{"key":"e_1_2_7_36_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tifs.2018.01.008"},{"key":"e_1_2_7_37_1","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1093\/genetics\/126.3.505","article-title":"Molecular evolution of the Escherichia coli chromosome. III. Clonal frames","volume":"126","author":"Milkman R.","year":"1990","journal-title":"Genetics"},{"key":"e_1_2_7_38_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2885"},{"key":"e_1_2_7_39_1","doi-asserted-by":"publisher","DOI":"10.3201\/eid2309.170336"},{"key":"e_1_2_7_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2016.185"},{"key":"e_1_2_7_41_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0997-x"},{"key":"e_1_2_7_42_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmm.2010.05.002"},{"key":"e_1_2_7_43_1","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2016.116"},{"key":"e_1_2_7_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.06.036"},{"key":"e_1_2_7_45_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2017.126"},{"key":"e_1_2_7_46_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000146"},{"key":"e_1_2_7_47_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01193-15"},{"key":"e_1_2_7_48_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.41.2.757-762.2003"},{"key":"e_1_2_7_49_1","unstructured":"Seemann T.(2018) Scan contig files against PubMLST typing schemes: tseemann\/mlst.https:\/\/github.com\/tseemann\/mlst."},{"key":"e_1_2_7_50_1","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2018.2586"},{"key":"e_1_2_7_51_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"e_1_2_7_52_1","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.00553-15"},{"key":"e_1_2_7_53_1","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.00106-16"},{"key":"e_1_2_7_54_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2014.05.006"},{"key":"e_1_2_7_55_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01127-08"},{"key":"e_1_2_7_56_1","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.00152-12"},{"key":"e_1_2_7_57_1","unstructured":"WHO. (2018)Listeriosis \u2013 South Africa. World Health Organization. URLhttps:\/\/www.who.int\/csr\/don\/28-march-2018-listeriosis-south-africa\/en\/."},{"key":"e_1_2_7_58_1","doi-asserted-by":"publisher","DOI":"10.1111\/2041-210X.12628"},{"key":"e_1_2_7_59_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr485"}],"container-title":["Environmental Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1111%2F1462-2920.15111","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1462-2920.15111","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/1462-2920.15111","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1462-2920.15111","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T04:30:43Z","timestamp":1761885043000},"score":1,"resource":{"primary":{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/10.1111\/1462-2920.15111"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,23]]},"references-count":58,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["10.1111\/1462-2920.15111"],"URL":"https:\/\/doi.org\/10.1111\/1462-2920.15111","archive":["Portico"],"relation":{},"ISSN":["1462-2912","1462-2920"],"issn-type":[{"value":"1462-2912","type":"print"},{"value":"1462-2920","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,23]]},"assertion":[{"value":"2020-02-26","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2020-05-30","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2020-06-23","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}