{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T11:46:26Z","timestamp":1784634386317,"version":"3.55.0"},"reference-count":43,"publisher":"Microbiology Society","issue":"5","license":[{"start":{"date-parts":[[2022,5,27]],"date-time":"2022-05-27T00:00:00Z","timestamp":1653609600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Medical Research Council","award":["MC_PC_16045"],"award-info":[{"award-number":["MC_PC_16045"]}]},{"DOI":"10.13039\/100010663","name":"H2020 European Research Council","doi-asserted-by":"crossref","award":["852957"],"award-info":[{"award-number":["852957"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/R012075\/1"],"award-info":[{"award-number":["BB\/R012075\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000691","name":"Academy of Medical Sciences","doi-asserted-by":"crossref","award":["SBF005\\1023"],"award-info":[{"award-number":["SBF005\\1023"]}],"id":[{"id":"10.13039\/501100000691","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,27]]},"abstract":"<jats:p>\n                    Genomic data contribute invaluable information to the epidemiological investigation of pathogens of public health importance. However, whole-genome sequencing (WGS) of bacteria typically relies on culture, which represents a major hurdle for generating such data for a wide range of species for which culture is challenging. In this study, we assessed the use of culture-free target-enrichment sequencing as a method for generating genomic data for two bacterial species: (1)\n                    <jats:italic>Bacillus anthracis,<\/jats:italic>\n                    which causes anthrax in both people and animals and whose culture requires high-level containment facilities; and (2)\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.9763\" xlink:type=\"simple\">Mycoplasma amphoriforme<\/jats:ext-link>\n                      <\/jats:named-content>\n                    <\/jats:italic>\n                    , a fastidious emerging human respiratory pathogen. We obtained high-quality genomic data for both species directly from clinical samples, with sufficient coverage (&gt;15\u00d7) for confident variant calling over at least 80% of the baited genomes for over two thirds of the samples tested. Higher qPCR cycle threshold (\n                    <jats:italic>Ct<\/jats:italic>\n                    ) values (indicative of lower pathogen concentrations in the samples), pooling libraries prior to capture, and lower captured library concentration were all statistically associated with lower capture efficiency. The\n                    <jats:italic>Ct<\/jats:italic>\n                    value had the highest predictive value, explaining 52\u200a% of the variation in capture efficiency. Samples with\n                    <jats:italic>Ct<\/jats:italic>\n                    values \u226430 were over six times more likely to achieve the threshold coverage than those with a\n                    <jats:italic>Ct<\/jats:italic>\n                    &gt; 30. We conclude that target-enrichment sequencing provides a valuable alternative to standard WGS following bacterial culture and creates opportunities for an improved understanding of the epidemiology and evolution of many clinically important pathogens for which culture is challenging.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.000836","type":"journal-article","created":{"date-parts":[[2022,5,27]],"date-time":"2022-05-27T13:16:16Z","timestamp":1653657376000},"source":"Crossref","is-referenced-by-count":11,"title":["Target-enrichment sequencing yields valuable genomic data for challenging-to-culture bacteria of public health importance"],"prefix":"10.1099","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0895-3549","authenticated-orcid":false,"given":"Tristan P. 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