{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T02:36:42Z","timestamp":1774406202950,"version":"3.50.1"},"reference-count":58,"publisher":"Microbiology Society","issue":"1","license":[{"start":{"date-parts":[[2025,1,7]],"date-time":"2025-01-07T00:00:00Z","timestamp":1736208000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100013373","name":"NIHR Oxford Biomedical Research Centre","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100013373","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,7]]},"abstract":"<jats:p>\n                  <jats:bold>Background.<\/jats:bold> The <jats:italic>Staphylococcus capitis<\/jats:italic> NRCS-A strain has emerged as a global cause of late-onset sepsis associated with outbreaks in neonatal intensive care units (NICUs) whose transmission is incompletely understood.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Methods.<\/jats:bold> Demographic and clinical data for 45 neonates with <jats:italic>S. capitis<\/jats:italic> and 90 with other coagulase-negative staphylococci (CoNS) isolated from sterile sites were reviewed, and clinical significance was determined. <jats:italic>S. capitis<\/jats:italic> isolated from 27 neonates at 2 hospitals between 2017 and 2022 underwent long-read (ONT) (<jats:italic>n<\/jats:italic>=27) and short-read (Illumina) sequencing (<jats:italic>n<\/jats:italic>=18). These sequences were compared with <jats:italic>S. capitis<\/jats:italic> sequenced from blood culture isolates from other adult and paediatric patients in the same hospitals (<jats:italic>n<\/jats:italic>=6), <jats:italic>S. capitis<\/jats:italic> isolated from surface swabs (found in 5\/150\u2009samples), rectal swabs (in 2\/69\u2009samples) in NICU patients and NICU environmental samples (in 5\/114\u2009samples). Reads from all samples were mapped to a hybrid assembly of a local sterile site strain, forming a complete UK NRCS-A reference genome, for outbreak analysis and comparison with 826 other <jats:italic>S. capitis<\/jats:italic> from the UK and Germany.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Results.<\/jats:bold>\n                  <jats:italic>S. capitis<\/jats:italic> bacteraemia was associated with increased length of NICU stay at sampling (median day 22 vs day 12 for other CoNS isolated; <jats:italic>P<\/jats:italic>=0.05). A phylogeny of sequenced <jats:italic>S. capitis<\/jats:italic> revealed a cluster comprised of 25\/27 neonatal sterile site isolates and 3\/5 superficial, 2\/2 rectal and 1\/5 environmental isolates. No isolates from other wards belonged to this cluster. Phylogenetic comparison with published sequences confirmed that the cluster was NRCS-A outbreak strain but found a relatively high genomic diversity (mean pairwise distance of 84.9 SNPs) and an estimated NRCS-A <jats:italic>S. capitis<\/jats:italic> molecular clock of 5.1 SNPs\/genome\/year (95% credibility interval 4.3\u20135.9). The presence of <jats:italic>S. capitis<\/jats:italic> in superficial cultures did not correlate with neonatal bacteraemia, but both neonates with rectal NRCS-A <jats:italic>S. capitis<\/jats:italic> carriage identified also experienced <jats:italic>S. capitis<\/jats:italic> bacteraemia.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Conclusions.<\/jats:bold>\n                  <jats:italic>S. capitis<\/jats:italic> bacteraemia occurred in patients with longer NICU admission than other CoNS. Genomic analysis confirms clinically significant infections with the NRCS-A <jats:italic>S. capitis<\/jats:italic> strain, distinct from non-NICU clinical samples. Multiple introductions of <jats:italic>S. capitis<\/jats:italic>, rather than prolonged environmental persistence, were seen over 5\u2009years of infections.<\/jats:p>","DOI":"10.1099\/mgen.0.001340","type":"journal-article","created":{"date-parts":[[2025,1,7]],"date-time":"2025-01-07T14:17:22Z","timestamp":1736259442000},"source":"Crossref","is-referenced-by-count":1,"title":["Multiple introductions of NRCS-A Staphylococcus capitis to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey"],"prefix":"10.1099","volume":"11","author":[{"given":"Emily A.","family":"Lees","sequence":"first","affiliation":[{"name":"Fitzwilliam College, Cambridge, UK"},{"name":"Department of Paediatrics, University of Oxford, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica","family":"Gentry","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Oxford University Hospitals, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hermione","family":"Webster","sequence":"additional","affiliation":[{"name":"National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), Oxford, UK"},{"name":"Nuffield Department of Medicine, University of Oxford, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas","family":"Sanderson","sequence":"additional","affiliation":[{"name":"National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), Oxford, UK"},{"name":"Nuffield Department of Medicine, University of Oxford, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Eyre","sequence":"additional","affiliation":[{"name":"Nuffield Department of Population Health, University of Oxford, Oxford, UK"},{"name":"National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Wilson","sequence":"additional","affiliation":[{"name":"Department for Continuing Education, University of Oxford, Oxford, UK"},{"name":"Nuffield Department of Population Health, University of Oxford, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sam","family":"Lipworth","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, University of Oxford, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Derrick","family":"Crook","sequence":"additional","affiliation":[{"name":"National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), Oxford, UK"},{"name":"Nuffield Department of Medicine, University of Oxford, Oxford, UK"},{"name":"Department of Microbiology, Oxford University Hospitals, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"T.H. 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