{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T10:54:07Z","timestamp":1790506447972,"version":"4.1.0"},"reference-count":21,"publisher":"Microbiology Society","issue":"4","license":[{"start":{"date-parts":[[2019,4,1]],"date-time":"2019-04-01T00:00:00Z","timestamp":1554076800000},"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":[[2019,4,1]]},"abstract":"\n The ability to distinguish different circulating pathogen clones from each other is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low-variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node. The utility of this software was demonstrated using both simulated outbreaks and real genomic data of two LV populations: a hospital outbreak of methicillin-resistant\n \n \n Staphylococcus aureus<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n and endemic\n \n \n Salmonella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n Typhi from rural Cambodia. rPinecone identified the transmission branches of the hospital outbreak and geographically confined lineages in Cambodia. Sub-lineages identified by rPinecone in both analyses were phylogenetically robust. It is anticipated that rPinecone can be used to discriminate between lineages of bacteria from LV populations where other methods fail, enabling a deeper understanding of infectious disease epidemiology for public health purposes.\n <\/jats:p>","DOI":"10.1099\/mgen.0.000264","type":"journal-article","created":{"date-parts":[[2019,3,28]],"date-time":"2019-03-28T09:12:49Z","timestamp":1553764369000},"source":"Crossref","is-referenced-by-count":16,"title":["rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree"],"prefix":"10.1099","volume":"5","author":[{"given":"Alexander M.","family":"Wailan","sequence":"first","affiliation":[{"name":"1\u200bParasites and Microbes, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesc","family":"Coll","sequence":"additional","affiliation":[{"name":"2\u200bLondon School of Hygiene & Tropical Medicine, Keppel St., London WC1E 7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eva","family":"Heinz","sequence":"additional","affiliation":[{"name":"1\u200bParasites and Microbes, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerry","family":"Tonkin-Hill","sequence":"additional","affiliation":[{"name":"1\u200bParasites and Microbes, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jukka","family":"Corander","sequence":"additional","affiliation":[{"name":"1\u200bParasites and Microbes, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK"},{"name":"3\u200bDepartment of Mathematics and Statistics, University of Helsinki, Helsinki, Finland"},{"name":"4\u200bDepartment of Biostatistics, University of Oslo, Oslo, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas A.","family":"Feasey","sequence":"additional","affiliation":[{"name":"5\u200bLiverpool School of Tropical Medicine, Pembroke Pl, Liverpool L3 5QA, UK"},{"name":"6\u200bMalawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas R.","family":"Thomson","sequence":"additional","affiliation":[{"name":"1\u200bParasites and Microbes, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK"},{"name":"2\u200bLondon School of Hygiene & Tropical Medicine, Keppel St., London WC1E 7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1093\/genetics\/155.2.945","article-title":"Inference of population structure using multilocus genotype data","volume":"155","author":"Pritchard","year":"2000","journal-title":"Genetics"},{"key":"R2","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1093\/genetics\/163.1.367","article-title":"Bayesian analysis of genetic differentiation between populations","volume":"163","author":"Corander","year":"2003","journal-title":"Genetics"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst028"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0004785"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(12)70268-2"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003457"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003537"},{"key":"R8","first-page":"583","article-title":"Cluster ensembles - 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