{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T18:30:28Z","timestamp":1783708228600,"version":"3.55.0"},"reference-count":63,"publisher":"Microbiology Society","issue":"1","license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"abstract":"<jats:p>The persuasiveness of genomic evidence has pressured scientific agencies to supplement or replace well-established methodologies to inform public health and food safety decision-making. This study of 52 epidemiologically defined <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.5096\" xlink:type=\"simple\">Listeria monocytogenes<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic> isolates, collected between 1981 and 2011, including nine outbreaks, was undertaken (1) to characterize their phylogenetic relationship at finished genome-level resolution, (2) to elucidate the underlying genetic diversity within an endemic subtype, CC8, and (3) to re-evaluate the genetic relationship and epidemiology of a CC8-delimited outbreak in Canada in 2008. Genomes representing Canadian <jats:italic>\n                     <jats:named-content content-type=\"genus\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.5095\" xlink:type=\"simple\">Listeria<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic> outbreaks between 1981 and 2010 were closed and manually annotated. Single nucleotide variants (SNVs) and horizontally acquired traits were used to generate phylogenomic models. Phylogenomic relationships were congruent with classical subtyping and epidemiology, except for CC8 outbreaks, wherein the distribution of SNV and prophages revealed multiple co-evolving lineages. Chronophyletic reconstruction of CC8 evolution indicates that prophage-related genetic changes among CC8 strains manifest as PFGE subtype reversions, obscuring the relationship between CC8 isolates, and complicating the public health interpretation of subtyping data, even at maximum genome resolution. The size of the shared genome interrogated did not change the genetic relationship measured between highly related isolates near the tips of the phylogenetic tree, illustrating the robustness of these approaches for routine public health applications where the focus is recent ancestry. The possibility exists for temporally and epidemiologically distinct events to appear related even at maximum genome resolution, highlighting the continued importance of epidemiological evidence.<\/jats:p>","DOI":"10.1099\/mgen.0.000237","type":"journal-article","created":{"date-parts":[[2019,1,16]],"date-time":"2019-01-16T15:13:52Z","timestamp":1547651632000},"source":"Crossref","is-referenced-by-count":12,"title":["Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria"],"prefix":"10.1099","volume":"5","author":[{"given":"Aleisha","family":"Reimer","sequence":"first","affiliation":[{"name":"1\u200bPublic Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly","family":"Weedmark","sequence":"additional","affiliation":[{"name":"2\u200bHealth Canada, Bureau of Microbial Hazards, Ottawa, ON, K1A 0K9, 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