{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T02:35:02Z","timestamp":1792118102226,"version":"4.4.0"},"reference-count":86,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2022,10,12]],"date-time":"2022-10-12T00:00:00Z","timestamp":1665532800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008287","name":"Science and Technology Directorate","doi-asserted-by":"publisher","award":["HSHQDC-17-C-B0021"],"award-info":[{"award-number":["HSHQDC-17-C-B0021"]}],"id":[{"id":"10.13039\/100008287","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009527","name":"Myndigheten f\u00f6r Samh\u00e4llsskydd och Beredskap","doi-asserted-by":"publisher","award":["TA014-2010-01"],"award-info":[{"award-number":["TA014-2010-01"]}],"id":[{"id":"10.13039\/100009527","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>\n                    <jats:italic>Francisella tularensis<\/jats:italic>\n                    , the bacterium that causes the zoonosis tularemia, and its genetic near neighbor species, can be difficult or impossible to cultivate from complex samples. Thus, there is a lack of genomic information for these species that has, among other things, limited the development of robust detection assays for\n                    <jats:italic>F<\/jats:italic>\n                    .\n                    <jats:italic>tularensis<\/jats:italic>\n                    that are both specific and sensitive. The objective of this study was to develop and validate approaches to capture, enrich, sequence, and analyze\n                    <jats:italic>Francisella<\/jats:italic>\n                    DNA present in DNA extracts generated from complex samples. RNA capture probes were designed based upon the known pan genome of\n                    <jats:italic>F<\/jats:italic>\n                    .\n                    <jats:italic>tularensis<\/jats:italic>\n                    and other diverse species in the family\n                    <jats:italic>Francisellaceae<\/jats:italic>\n                    . Probes that targeted genomic regions also present in non-\n                    <jats:italic>Francisellaceae<\/jats:italic>\n                    species were excluded, and probes specific to particular\n                    <jats:italic>Francisella<\/jats:italic>\n                    species or phylogenetic clades were identified. The capture-enrichment system was then applied to diverse, complex DNA extracts containing low-level\n                    <jats:italic>Francisella<\/jats:italic>\n                    DNA, including human clinical tularemia samples, environmental samples (\n                    <jats:italic>i<\/jats:italic>\n                    .\n                    <jats:italic>e<\/jats:italic>\n                    ., animal tissue and air filters), and whole ticks\/tick cell lines, which was followed by sequencing of the enriched samples. Analysis of the resulting data facilitated rigorous and unambiguous confirmation of the detection of\n                    <jats:italic>F<\/jats:italic>\n                    .\n                    <jats:italic>tularensis<\/jats:italic>\n                    or other\n                    <jats:italic>Francisella<\/jats:italic>\n                    species in complex samples, identification of mixtures of different\n                    <jats:italic>Francisella<\/jats:italic>\n                    species in the same sample, analysis of gene content (\n                    <jats:italic>e<\/jats:italic>\n                    .\n                    <jats:italic>g<\/jats:italic>\n                    ., known virulence and antimicrobial resistance loci), and high-resolution whole genome-based genotyping. The benefits of this capture-enrichment system include: even very low target DNA can be amplified; it is culture-independent, reducing exposure for research and\/or clinical personnel and allowing genomic information to be obtained from samples that do not yield isolates; and the resulting comprehensive data not only provide robust means to confirm the presence of a target species in a sample, but also can provide data useful for source attribution, which is important from a genomic epidemiology perspective.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0273273","type":"journal-article","created":{"date-parts":[[2022,10,12]],"date-time":"2022-10-12T13:34:03Z","timestamp":1665581643000},"page":"e0273273","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Genomic characterization of Francisella tularensis and other diverse Francisella species from complex samples"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2684-6007","authenticated-orcid":true,"given":"David M.","family":"Wagner","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dawn N.","family":"Birdsell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryelan F.","family":"McDonough","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roxanne","family":"Nottingham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karisma","family":"Kocos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimberly","family":"Celona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasemin","family":"\u00d6zs\u00fcrekci","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8489-757X","authenticated-orcid":true,"given":"Caroline","family":"\u00d6hrman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda","family":"Karlsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerstin","family":"Myrtenn\u00e4s","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Sj\u00f6din","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0548-5943","authenticated-orcid":true,"given":"Anders","family":"Johansson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul 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