Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates

Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Data Note Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates Yu Wan, Rachel Pike, Alessandra Harley, Zaynab Mumin, Isabelle Potterill, and 11 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4808318/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 15 Feb, 2025 Read the published version in BMC Genomic Data → Version 1 posted 9 You are reading this latest preprint version Abstract Objective Staphylococcus capitis is part of the human microbiome and an opportunistic pathogen known to cause catheter-associated bacteraemia, prosthetic joint infections, skin and wound infections, among others. Detection of S. capitis in normally sterile body sites saw an increase over the last decade in England, where a multidrug-resistant clone, NRCS-A, was widely identified in blood samples from infants in neonatal intensive care units. To address a lack of complete genomes and antibiograms of S. capitis in public databases, we performed long- and short-read whole-genome sequencing, hybrid genome assembly, and antimicrobial susceptibility testing of 22 diverse isolates. Data description We present complete genome assemblies of two S. capitis type strains (subspecies capitis : DSM 20326; subspecies urealyticus : DSM 6717) and 20 clinical isolates (NRCS-A: 10) from England. Each genome is accompanied by minimum inhibitory concentrations of 13 antimicrobials including vancomycin, teicoplanin, daptomycin, linezolid, and clindamycin. These 22 genomes were 2.4–2.7 Mbp in length and had a GC content of 33%. Plasmids were identified in 20 isolates. Resistance to teicoplanin, daptomycin, gentamicin, fusidic acid, rifampicin, ciprofloxacin, clindamycin, and erythromycin was seen in 1–10 isolates. Our data are a resource for future studies on genomics, evolution, and antimicrobial resistance of S. capitis . Staphylococcus capitis reference genomes hybrid genome assembly antimicrobial susceptibility antimicrobial resistance antibiograms bioresource genomics NRCS-A clone Nanopore MinION sequencing Objective Staphylococcus capitis , consisting of two subspecies capitis and urealyticus [ 1 , 2 ], is a coagulase-negative opportunistic pathogen commonly causing late-onset sepsis (LOS) in very-low-birthweight infants in neonatal intensive care units (NICUs) and various infections in adults, such as prosthetic joint infections [ 3 , 4 ]. A multidrug-resistant clone of S. capitis subsp. urealyticus , NRCS-A, has emerged as a global concern in neonatal health for its dominance in LOS, reduced susceptibility to vancomycin, enhanced biofilm-forming ability, increased disinfectant and desiccation tolerance, association with neonatal incubators, and persistence in NICUs [ 5 – 7 ]. Between 2020 and 2021, the UK Health Security Agency (UKHSA) convened a nationwide investigation into increased reporting of neonatal S. capitis bacteraemia in England [ 8 ] and requested voluntary referral of clinical isolates from diagnostic laboratories for whole-genome sequencing (WGS). Genomic epidemiological analysis of the WGS data revealed widespread presence of the NRCS-A clone in neonatal units across the country, highlighting the need to further understand genomics, antimicrobial resistance (AMR), and niche adaptation of this clone in comparison with other S. capitis subpopulations [ 9 ]. In this report, we describe complete genome assemblies and accompanying antibiograms of 22 S. capitis isolates consisting of 20 English clinical isolates and type strains of the two subspecies ( capitis : DSM 20326; urealyticus : DSM 6717). The clinical isolates were selected from UKHSA’s culture collection to represent the main S. capitis subpopulations previously identified (Figure S1 ) [ 9 ], with 19 of these isolates recovered from normally sterile sites in patients across England. Readers are referred to Table S1 for source information of isolates. Altogether, 10 NRCS-A isolates and 12 non-NRCS-A isolates were sequenced. Our work addresses the lack of finished-grade S. capitis reference genomes and antibiograms in the National Center for Biotechnology Information (NCBI) databases, providing a bioresource for future studies on the genomics, AMR, molecular epidemiology, and evolution of S. capitis . Data description Each isolate was incubated on Columbia agar with horse blood (PB0122A, Thermo Scientific, UK) at 37°C overnight for DNA extraction and antimicrobial susceptibility testing in 2021 (Batch 1, 19 isolates) or 2023 (Batch 2, three isolates) (Table S2 ). For Batch 1, genomic DNA of each isolate was extracted using GeneJET Genomic DNA Purification Kits (Thermo Scientific). Long-read WGS was conducted with Oxford Nanopore Technologies (ONT, UK) MinION R9.4.1 flow-cells (FLO-MIN106D) and Rapid Barcoding Kits (SQK-RBK004). High-accuracy basecalling was performed with guppy (ONT). Short-read sequencing of the same DNA was performed on Illumina HiSeq 2500 systems at the UKHSA following an in-house 2×101 bp protocol. For Batch 2, genomic DNA was extracted using a Wizard Genomic DNA Purification Kit (Promega, USA). Long-read WGS was conducted with an ONT MinION R10.4.1 flow-cell (FLO-MIN114) and Rapid Barcoding Kit 24 V14 (SQK-RBK114.24). Super-accuracy basecalling was performed using guppy. Short-read sequencing of the same DNA was performed under a 2×251 bp layout on Illumina NovaSeq 6000 systems at MicrobesNG (UK). Susceptibility of isolates to 13 antimicrobials was determined by the UKHSA Antimicrobial Resistance and Healthcare Associated Infections Reference Unit with gradient strips (Liofilchem, Italy, for Batch 1) or broth microdilution (EUSTAPF, Thermo Scientific, for Batch 2) following European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines (Batch 1, v11.0; Batch 2, v13.1). Inducible clindamycin resistance was sought by testing for the antagonism between erythromycin and clindamycin (D-test). ONT reads were trimmed with fastp and filtered with nanoq for quality control [ 10 , 11 ]. Illumina reads were trimmed and filtered with fastp [ 12 ]. Hybrid de novo genome assembly was performed with an ONT-reads-first strategy using Flye, Raven, and minipolish as implemented in Trycycler [ 13 – 16 ] or only using Raven, according to estimated read depths. Alternatively, an Illumina-reads-first strategy was applied using Unicycler when a genome could not be fully assembled from ONT reads [ 17 , 18 ]. All assemblies were polished with ONT reads using medaka (github.com/nanoporetech/medaka) followed by Illumina-read polishing using Polypolish and POLCA [ 19 , 20 ]. Polished assemblies were then were reoriented to start from dnaA (chromosomes) or repA (plasmids) genes using dnaapler [ 21 ]. Reoriented assemblies were polished with Illumina reads using Polypolish, assessed using Quast and CheckM2 [ 22 , 23 ], and annotated with the NCBI Prokaryotic Genome Annotation Pipeline [ 24 ]. Twenty-two complete genome assemblies were generated, with the same GC content of 33% and lengths of 2.4–2.7 Mbp (Table S2 ). One to four plasmids (2.3–69 kbp) were identified in 20 isolates (NRCS-A: 9; non-NRCS-A: 11). The NRCS-A clone exhibited reduced susceptibility to teicoplanin, daptomycin, and gentamicin (Table S3 ). Resistance to fusidic acid (MICs: 16–32 mg/L), erythromycin (MIC > 256 mg/L), and clindamycin (MIC > 256 mg/L or inducible) was seen in 9/22 (41%), 7/22 (32%), and 5/22 (23%) of isolates, respectively, with no significant frequency difference between NRCS-A and non-NRCS-A isolates (p-value = 1, Fisher’s exact test). One NRCS-A isolate exhibited rifampicin resistance (MIC > 32 mg/L). All isolates were susceptible to vancomycin, linezolid, and quinupristin-dalfopristin, and seven non-NRCS-A isolates, including the two type strains, were susceptible to all 11 antimicrobials having EUCAST breakpoints. Table 1 Overview of datafiles/datasets Label Name of data file/data set File types (file extension) Data repository and identifier (DOI or accession number) Datafile 1 Figure S1 , Genetic relatedness between the 22 selected isolates within the context of 838 isolates previously analysed Portable Document Format file (.pdf) figshare, DOI: 10.6084/m9.figshare.26048464 [ 25 ] Datafile 2 Table S1 , sources and data accessions of S. capitis isolates MS Excel file (.xlsx) figshare, DOI: 10.6084/m9.figshare.26049013 [ 26 ] Datafile 3 Table S2 , methods and summary statistics of genome assemblies MS Excel file (.xlsx) figshare, DOI: 10.6084/m9.figshare.26049070 [ 27 ] Datafile 4 Table S3 , antibiograms of isolates MS Excel file (.xlsx) figshare, DOI: 10.6084/m9.figshare.26049094 [ 28 ] Dataset 1 Illumina and ONT reads, and annotated genome assemblies SRA (.sra) and GenBank files (.gbk) NCBI BioProject PRJNA1032276 [ 29 ] Limitations This dataset is limited to a small sample size (n = 22), which does not capture all major phenotypic and genetic variations in S. capitis . The isolates are limited to England and dominated by invasive isolates (n = 19) recovered from normally sterile body sites of humans — eight (42%) invasive isolates were collected from infants of ≤ 90 days of age, one (5%) from an infant between > 90 days and < 1 year of age, two (10%) from children between six and 11 years of age, and eight from adults (≥ 18 years of age). Moreover, antimicrobial susceptibility of all isolates in Batch 1 (n = 19) was not determined using the gold-standard method, broth microdilution. Future work needs to elucidate mechanisms of AMR [ 30 ] and include a wider range of isolates, such as those recovered from carriage screening, environments, animals, and other health-related samples from non-clinical settings. Abbreviations AMR Antimicrobial resistance BRC Biomedical Research Centre DSM Deutsche Sammlung von Mikroorganismen EUCAST European Committee on Antimicrobial Susceptibility Testing HPRU Health Protection Research Unit LOS Late-onset sepsis NCBI National Center for Biotechnology Information NICU Neonatal intensive care unit NIHR National Institute for Health Research ONT Oxford Nanopore Technologies WGS Whole-genome sequencing UKHSA UK Health Security Agency Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Availability of data and materials Data generated in this study are listed in Table 1. Specifically, sequence data and antibiograms have been deposited in NCBI databases under the BioProject accession PRJNA1032276. Antibiograms are accessible in BioSample records of the isolates. Competing interests The authors declare no completing interests. Funding This work was mainly funded by the UKHSA and partially funded by the Wellcome Trust and Imperial College London through Y. Wan’s Imperial Institutional Strategic Support Fund Springboard Research Fellowship (grant number: PSN109). Y. Wan is a David Price Evans Research Fellow in Global Health and Infectious Diseases, funded by the University of Liverpool. Professor A. H. Holmes is a National Institute for Health and Care Research (NIHR) Senior Investigator and is affiliated with the Department of Health and Social Care funded Centre for Antimicrobial Optimisation at Imperial College London. Y. Wan, D. Meunier, M. Getino, E. Jauneikaite, A. H. Holmes, C. S. Brown, A. Demirjian, K. L. Hopkins, and B. Pichon are affiliated with the National Institute for Health and Care Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London in partnership with the UKHSA, in collaboration with, Imperial Healthcare Partners, University of Cambridge and University of Warwick (grant number: NIHR200876). The views expressed in this article are those of the authors and not necessarily those of the NHS, the National Institute for Health Research, or the Department of Health and Social Care. Authors’ contributions Conceptualisation: Y. Wan, B. Pichon; resources: B. Pichon, K. L. Hopkins, J. Coelho, E. Jauneikaite, K. Moganeradj; investigation: Y. Wan, R. Pike, A. Harley, Z. Mumin, I. Potterill, D. Meunier, M. Ganner, M. Getino, K. L. Hopkins; supervision: B. Pichon, K. L. Hopkins, J. Coelho, A. Demirjian, C. S. Brown, A. H. Holmes, E. Jauneikaite, K. Moganeradj; funding acquisition: C. S. Brown, Y. Wan, A. H. Holmes, E. Jauneikaite. Writing, first draft: Y. Wan; editing: Y. Wan, D. Meunier, R. Pike, E. Jauneikaite, A. Demirjian, C. S. Brown, B. Pichon, K. L. Hopkins, K. Moganeradj, M. Ganner; approval of the final manuscript: All. Acknowledgements All authors thank microbiology laboratories and clinicians across the UK for sharing S. capitis isolates and specimen information. Illumina WGS of isolates in Batch 1 was carried out by the Colindale Sequencing Laboratory at the UKHSA. Part of the microbiological work, sample preparation, ONT sequencing, and bioinformatics analysis was undertaken at the Colebrook Laboratory, a facility supported by the NIHR Imperial Biomedical Research Centre (BRC). Part of bioinformatics analysis was performed on equipment purchased as part of MRC CARP fellowship award MR/T005254/1. References Kloos WE, Schleifer KH. Isolation and Characterization of Staphylococci from Human Skin II. Descriptions of Four New Species: Staphylococcus warneri , Staphylococcus capitis , Staphylococcus hominis , and Staphylococcus simulans 1. International Journal of Systematic and Evolutionary Microbiology. 1975;25:62–79. Bannerman TL, Kloos WE. Staphylococcus capitis subsp. ureolyticus subsp. nov. from Human Skin. International Journal of Systematic and Evolutionary Microbiology. 1991;41:144–7. Butin M, Martins-Simões P, Rasigade J-P, Picaud J-C, Laurent F. Worldwide Endemicity of a Multidrug-Resistant Staphylococcus capitis Clone Involved in Neonatal Sepsis. Emerg Infect Dis. 2017;23:538–9. Tevell S, Baig S, Hellmark B, Martins Simoes P, Wirth T, Butin M, et al. Presence of the neonatal Staphylococcus capitis outbreak clone (NRCS-A) in prosthetic joint infections. Sci Rep. 2020;10:22389. Rasigade J-P, Raulin O, Picaud J-C, Tellini C, Bes M, Grando J, et al. Methicillin-Resistant Staphylococcus capitis with Reduced Vancomycin Susceptibility Causes Late-Onset Sepsis in Intensive Care Neonates. PLoS ONE. 2012;7:e31548. Chavignon M, Coignet L, Bonhomme M, Bergot M, Tristan A, Verhoeven P, et al. Environmental Persistence of Staphylococcus capitis NRCS-A in Neonatal Intensive Care Units: Role of Biofilm Formation, Desiccation, and Disinfectant Tolerance. Microbiol Spectr. 2022;10:e04215–22. Moore G, Barry A, Carter J, Ready J, Wan Y, Elsayed M, et al. Detection, survival, and persistence of Staphylococcus capitis NRCS-A in neonatal units in England. J Hosp Infect. 2023;140:8–14. Paranthaman K, Wilson A, Verlander N, Rooney G, Macdonald N, Nsonwu O, et al. Trends in coagulase-negative staphylococci (CoNS), England, 2010–2021. Access Microbiol. 2023;5:000491v3. Wan Y, Ganner M, Mumin Z, Ready D, Moore G, Potterill I, et al. 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CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods. 2023;20:1203–12. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44:6614–24. Wan Y, Ganner M, Pike R, Mumin Z, Potterill I, Meunier D et al. Figure S1, genetic relatedness between the 22 selected isolates within the context of 838 isolates previously analysed. 2024. https://doi.org/10.6084/m9.figshare.26048464 Wan Y, Ganner M, Pike R, Mumin Z, Potterill I, Meunier D et al. Table S1, sources and data accessions of S. capitis isolates. 2024. https://doi.org/10.6084/m9.figshare.26049013 Wan Y, Ganner M, Pike R, Mumin Z, Potterill I, Meunier D et al. Table S2, methods and summary statistics of genome assemblies. 2024. https://doi.org/10.6084/m9.figshare.26049070 Wan Y, Ganner M, Pike R, Mumin Z, Potterill I, Meunier D et al. Table S3, antibiograms of isolates. 2024. https://doi.org/10.6084/m9.figshare.26049094 Wan Y, Ganner M, Pike R, Mumin Z, Potterill I, Meunier D et al. Staphylococcus capitis reference genomes. 2024. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1032276 Chindelevitch L, van Dongen M, Graz H, Pedrotta A, Suresh A, Uplekar S, et al. Ten simple rules for the sharing of bacterial genotype—Phenotype data on antimicrobial resistance. PLoS Comput Biol. 2023;19:e1011129. Additional Declarations No competing interests reported. Supplementary Files FigureS1rev2.eps TableS1rev2.xlsx TableS2rev22.xlsx TableS3rev2.xlsx Cite Share Download PDF Status: Published Journal Publication published 15 Feb, 2025 Read the published version in BMC Genomic Data → Version 1 posted Editorial decision: Revision requested 17 Oct, 2024 Reviews received at journal 16 Oct, 2024 Reviewers agreed at journal 02 Oct, 2024 Reviews received at journal 23 Aug, 2024 Reviewers agreed at journal 21 Aug, 2024 Reviewers invited by journal 20 Aug, 2024 Editor assigned by journal 31 Jul, 2024 Submission checks completed at journal 31 Jul, 2024 First submitted to journal 26 Jul, 2024 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4808318","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Data Note","associatedPublications":[],"authors":[{"id":345082803,"identity":"f49f51e2-9d5e-4602-9aa8-efe305719e23","order_by":0,"name":"Yu Wan","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA5UlEQVRIiWNgGAWjYPACGxk2KEsGQh0gqCWNB6aFh1gth3lgLMJaDG4ksEn83HGeh08i+djnggobHgb2ww+Yec7g1yLZe+Y2D5tEWvLsGWfSeBh40gyYeW7g13KDtw2oheeMMTNvG8iFOQzMPB/wa7n5t+0cUMv5zxAt/G8Ia7nN23aAh429hxmiRQJkCx6HSZ552P5bti0ZqKXNmBnkFzaJZwYH5+DxPt/x5MOGb9vs5OSbmR8zA0NMjp8/+eGDN8dwa1E4wNgA5zCDCFCcHsCtgYFBvgGJw4xP5SgYBaNgFIxcAADEfkc19TVyCQAAAABJRU5ErkJggg==","orcid":"","institution":"University of Liverpool","correspondingAuthor":true,"prefix":"","firstName":"Yu","middleName":"","lastName":"Wan","suffix":""},{"id":345082804,"identity":"dce0ea7a-458a-4f58-9581-33f9c3f204fd","order_by":1,"name":"Rachel Pike","email":"","orcid":"","institution":"UK Health Security Agency","correspondingAuthor":false,"prefix":"","firstName":"Rachel","middleName":"","lastName":"Pike","suffix":""},{"id":345082805,"identity":"95cc195b-78e6-4dd1-b01c-e62936082b31","order_by":2,"name":"Alessandra Harley","email":"","orcid":"","institution":"UK Health Security Agency","correspondingAuthor":false,"prefix":"","firstName":"Alessandra","middleName":"","lastName":"Harley","suffix":""},{"id":345082806,"identity":"03988fa4-ba8b-47e7-94c8-677a7cb593f5","order_by":3,"name":"Zaynab Mumin","email":"","orcid":"","institution":"UK Health Security Agency","correspondingAuthor":false,"prefix":"","firstName":"Zaynab","middleName":"","lastName":"Mumin","suffix":""},{"id":345082807,"identity":"de252cf4-f922-4eeb-8215-fa119f50515c","order_by":4,"name":"Isabelle Potterill","email":"","orcid":"","institution":"UK Health Security Agency","correspondingAuthor":false,"prefix":"","firstName":"Isabelle","middleName":"","lastName":"Potterill","suffix":""},{"id":345082808,"identity":"a9b31d31-6959-46f8-904c-455ccd5a8e9b","order_by":5,"name":"Danièle Meunier","email":"","orcid":"","institution":"UK Health Security Agency","correspondingAuthor":false,"prefix":"","firstName":"Danièle","middleName":"","lastName":"Meunier","suffix":""},{"id":345082813,"identity":"e5ef94c9-952e-46fc-83df-875a5e33f07a","order_by":6,"name":"Mark Ganner","email":"","orcid":"","institution":"UK Health Security Agency","correspondingAuthor":false,"prefix":"","firstName":"Mark","middleName":"","lastName":"Ganner","suffix":""},{"id":345082815,"identity":"8409ae78-75f5-43f4-b072-7c55e3a913aa","order_by":7,"name":"Maria Getino","email":"","orcid":"","institution":"UK Health Security Agency","correspondingAuthor":false,"prefix":"","firstName":"Maria","middleName":"","lastName":"Getino","suffix":""},{"id":345082818,"identity":"e49f3855-a700-48a8-948d-0aef0dc43aa9","order_by":8,"name":"Juliana Coelho","email":"","orcid":"","institution":"UK Health Security Agency","correspondingAuthor":false,"prefix":"","firstName":"Juliana","middleName":"","lastName":"Coelho","suffix":""},{"id":345082823,"identity":"7d5ba4ce-3803-4420-8abd-644e187bbbc0","order_by":9,"name":"Elita Jauneikaite","email":"","orcid":"","institution":"Imperial College London","correspondingAuthor":false,"prefix":"","firstName":"Elita","middleName":"","lastName":"Jauneikaite","suffix":""},{"id":345082824,"identity":"0631b616-20cc-40ea-82e0-68dde4a8b080","order_by":10,"name":"Kartyk Moganeradj","email":"","orcid":"","institution":"UK Health Security Agency","correspondingAuthor":false,"prefix":"","firstName":"Kartyk","middleName":"","lastName":"Moganeradj","suffix":""},{"id":345082825,"identity":"5d3cbdae-3a40-4587-800d-9db14717b179","order_by":11,"name":"Colin S. 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Hopkins","email":"","orcid":"","institution":"Imperial College London","correspondingAuthor":false,"prefix":"","firstName":"Katie","middleName":"L.","lastName":"Hopkins","suffix":""},{"id":345082829,"identity":"da5200d9-f585-4635-ad32-4e2bc3fa6ab4","order_by":15,"name":"Bruno Pichon","email":"","orcid":"","institution":"UK Health Security Agency","correspondingAuthor":false,"prefix":"","firstName":"Bruno","middleName":"","lastName":"Pichon","suffix":""}],"badges":[],"createdAt":"2024-07-26 13:14:34","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4808318/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4808318/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12863-025-01303-8","type":"published","date":"2025-02-15T15:57:18+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":76487468,"identity":"c7eb8a09-bb7b-43e3-82b3-b6ef97a8931b","added_by":"auto","created_at":"2025-02-17 16:07:53","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":546504,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4808318/v1/dd73b411-7603-4442-92fc-ffdfdbf83755.pdf"},{"id":63403405,"identity":"82a2a95e-6a28-48ce-95f6-c98d419178ce","added_by":"auto","created_at":"2024-08-27 19:37:49","extension":"eps","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":333913,"visible":true,"origin":"","legend":"","description":"","filename":"FigureS1rev2.eps","url":"https://assets-eu.researchsquare.com/files/rs-4808318/v1/e18cb94dd342e68b7557e1c8.eps"},{"id":63403403,"identity":"c908f5c7-7461-42ae-b51e-a038d7cea6df","added_by":"auto","created_at":"2024-08-27 19:37:49","extension":"xlsx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":16617,"visible":true,"origin":"","legend":"","description":"","filename":"TableS1rev2.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-4808318/v1/293116ac2a7d9840a0501454.xlsx"},{"id":63403596,"identity":"3e1f91a3-e319-474a-9aa1-21362866aea6","added_by":"auto","created_at":"2024-08-27 19:45:49","extension":"xlsx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":17942,"visible":true,"origin":"","legend":"","description":"","filename":"TableS2rev22.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-4808318/v1/b6c0b470ded1a263420292b9.xlsx"},{"id":63403597,"identity":"182369b0-8613-415f-937e-922a9c788e86","added_by":"auto","created_at":"2024-08-27 19:45:49","extension":"xlsx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":70640,"visible":true,"origin":"","legend":"","description":"","filename":"TableS3rev2.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-4808318/v1/e1496855b9972496da18f4a1.xlsx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates","fulltext":[{"header":"Objective","content":"\u003cp\u003e \u003cem\u003eStaphylococcus capitis\u003c/em\u003e, consisting of two subspecies \u003cem\u003ecapitis\u003c/em\u003e and \u003cem\u003eurealyticus\u003c/em\u003e [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e], is a coagulase-negative opportunistic pathogen commonly causing late-onset sepsis (LOS) in very-low-birthweight infants in neonatal intensive care units (NICUs) and various infections in adults, such as prosthetic joint infections [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. A multidrug-resistant clone of \u003cem\u003eS. capitis\u003c/em\u003e subsp. \u003cem\u003eurealyticus\u003c/em\u003e, NRCS-A, has emerged as a global concern in neonatal health for its dominance in LOS, reduced susceptibility to vancomycin, enhanced biofilm-forming ability, increased disinfectant and desiccation tolerance, association with neonatal incubators, and persistence in NICUs [\u003cspan additionalcitationids=\"CR6\" citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e]. Between 2020 and 2021, the UK Health Security Agency (UKHSA) convened a nationwide investigation into increased reporting of neonatal \u003cem\u003eS. capitis\u003c/em\u003e bacteraemia in England [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e] and requested voluntary referral of clinical isolates from diagnostic laboratories for whole-genome sequencing (WGS). Genomic epidemiological analysis of the WGS data revealed widespread presence of the NRCS-A clone in neonatal units across the country, highlighting the need to further understand genomics, antimicrobial resistance (AMR), and niche adaptation of this clone in comparison with other \u003cem\u003eS. capitis\u003c/em\u003e subpopulations [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn this report, we describe complete genome assemblies and accompanying antibiograms of 22 \u003cem\u003eS. capitis\u003c/em\u003e isolates consisting of 20 English clinical isolates and type strains of the two subspecies (\u003cem\u003ecapitis\u003c/em\u003e: DSM 20326; \u003cem\u003eurealyticus\u003c/em\u003e: DSM 6717). The clinical isolates were selected from UKHSA\u0026rsquo;s culture collection to represent the main \u003cem\u003eS. capitis\u003c/em\u003e subpopulations previously identified (Figure \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e) [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e], with 19 of these isolates recovered from normally sterile sites in patients across England. Readers are referred to Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e for source information of isolates. Altogether, 10 NRCS-A isolates and 12 non-NRCS-A isolates were sequenced. Our work addresses the lack of finished-grade \u003cem\u003eS. capitis\u003c/em\u003e reference genomes and antibiograms in the National Center for Biotechnology Information (NCBI) databases, providing a bioresource for future studies on the genomics, AMR, molecular epidemiology, and evolution of \u003cem\u003eS. capitis\u003c/em\u003e.\u003c/p\u003e"},{"header":"Data description","content":"\u003cp\u003eEach isolate was incubated on Columbia agar with horse blood (PB0122A, Thermo Scientific, UK) at 37\u0026deg;C overnight for DNA extraction and antimicrobial susceptibility testing in 2021 (Batch 1, 19 isolates) or 2023 (Batch 2, three isolates) (Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e). For Batch 1, genomic DNA of each isolate was extracted using GeneJET Genomic DNA Purification Kits (Thermo Scientific). Long-read WGS was conducted with Oxford Nanopore Technologies (ONT, UK) MinION R9.4.1 flow-cells (FLO-MIN106D) and Rapid Barcoding Kits (SQK-RBK004). High-accuracy basecalling was performed with guppy (ONT). Short-read sequencing of the same DNA was performed on Illumina HiSeq 2500 systems at the UKHSA following an in-house 2\u0026times;101 bp protocol. For Batch 2, genomic DNA was extracted using a Wizard Genomic DNA Purification Kit (Promega, USA). Long-read WGS was conducted with an ONT MinION R10.4.1 flow-cell (FLO-MIN114) and Rapid Barcoding Kit 24 V14 (SQK-RBK114.24). Super-accuracy basecalling was performed using guppy. Short-read sequencing of the same DNA was performed under a 2\u0026times;251 bp layout on Illumina NovaSeq 6000 systems at MicrobesNG (UK). Susceptibility of isolates to 13 antimicrobials was determined by the UKHSA Antimicrobial Resistance and Healthcare Associated Infections Reference Unit with gradient strips (Liofilchem, Italy, for Batch 1) or broth microdilution (EUSTAPF, Thermo Scientific, for Batch 2) following European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines (Batch 1, v11.0; Batch 2, v13.1). Inducible clindamycin resistance was sought by testing for the antagonism between erythromycin and clindamycin (D-test).\u003c/p\u003e \u003cp\u003eONT reads were trimmed with fastp and filtered with nanoq for quality control [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e, \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. Illumina reads were trimmed and filtered with fastp [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. Hybrid \u003cem\u003ede novo\u003c/em\u003e genome assembly was performed with an ONT-reads-first strategy using Flye, Raven, and minipolish as implemented in Trycycler [\u003cspan additionalcitationids=\"CR14 CR15\" citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e] or only using Raven, according to estimated read depths. Alternatively, an Illumina-reads-first strategy was applied using Unicycler when a genome could not be fully assembled from ONT reads [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e, \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. All assemblies were polished with ONT reads using medaka (github.com/nanoporetech/medaka) followed by Illumina-read polishing using Polypolish and POLCA [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e, \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e]. Polished assemblies were then were reoriented to start from \u003cem\u003ednaA\u003c/em\u003e (chromosomes) or \u003cem\u003erepA\u003c/em\u003e (plasmids) genes using dnaapler [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. Reoriented assemblies were polished with Illumina reads using Polypolish, assessed using Quast and CheckM2 [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e, \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e], and annotated with the NCBI Prokaryotic Genome Annotation Pipeline [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eTwenty-two complete genome assemblies were generated, with the same GC content of 33% and lengths of 2.4\u0026ndash;2.7 Mbp (Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e). One to four plasmids (2.3\u0026ndash;69 kbp) were identified in 20 isolates (NRCS-A: 9; non-NRCS-A: 11). The NRCS-A clone exhibited reduced susceptibility to teicoplanin, daptomycin, and gentamicin (Table \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e). Resistance to fusidic acid (MICs: 16\u0026ndash;32 mg/L), erythromycin (MIC\u0026thinsp;\u0026gt;\u0026thinsp;256 mg/L), and clindamycin (MIC\u0026thinsp;\u0026gt;\u0026thinsp;256 mg/L or inducible) was seen in 9/22 (41%), 7/22 (32%), and 5/22 (23%) of isolates, respectively, with no significant frequency difference between NRCS-A and non-NRCS-A isolates (p-value\u0026thinsp;=\u0026thinsp;1, Fisher\u0026rsquo;s exact test). One NRCS-A isolate exhibited rifampicin resistance (MIC\u0026thinsp;\u0026gt;\u0026thinsp;32 mg/L). All isolates were susceptible to vancomycin, linezolid, and quinupristin-dalfopristin, and seven non-NRCS-A isolates, including the two type strains, were susceptible to all 11 antimicrobials having EUCAST breakpoints.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eOverview of datafiles/datasets\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"4\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eLabel\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eName of data file/data set\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eFile types\u003c/p\u003e \u003cp\u003e(file extension)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eData repository and identifier (DOI or accession number)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eDatafile 1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFigure \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e, Genetic relatedness between the 22 selected isolates within the context of 838 isolates previously analysed\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ePortable Document Format file (.pdf)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003efigshare, DOI: \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.6084/m9.figshare.26048464\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.26048464\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eDatafile 2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTable \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e, sources and data accessions of \u003cem\u003eS. capitis\u003c/em\u003e isolates\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMS Excel file (.xlsx)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003efigshare, DOI: \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.6084/m9.figshare.26049013\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.26049013\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eDatafile 3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTable \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e, methods and summary statistics of genome assemblies\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMS Excel file (.xlsx)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003efigshare, DOI: \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.6084/m9.figshare.26049070\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.26049070\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eDatafile 4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTable \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e, antibiograms of isolates\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMS Excel file (.xlsx)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003efigshare, DOI: \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.6084/m9.figshare.26049094\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.26049094\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eDataset 1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eIllumina and ONT reads, and annotated genome assemblies\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eSRA (.sra) and GenBank files (.gbk)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eNCBI BioProject PRJNA1032276 [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e"},{"header":"Limitations","content":"\u003cp\u003eThis dataset is limited to a small sample size (n\u0026thinsp;=\u0026thinsp;22), which does not capture all major phenotypic and genetic variations in \u003cem\u003eS. capitis\u003c/em\u003e. The isolates are limited to England and dominated by invasive isolates (n\u0026thinsp;=\u0026thinsp;19) recovered from normally sterile body sites of humans \u0026mdash; eight (42%) invasive isolates were collected from infants of \u0026le;\u0026thinsp;90 days of age, one (5%) from an infant between \u0026gt;\u0026thinsp;90 days and \u0026lt;\u0026thinsp;1 year of age, two (10%) from children between six and 11 years of age, and eight from adults (\u0026ge;\u0026thinsp;18 years of age). Moreover, antimicrobial susceptibility of all isolates in Batch 1 (n\u0026thinsp;=\u0026thinsp;19) was not determined using the gold-standard method, broth microdilution. Future work needs to elucidate mechanisms of AMR [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e] and include a wider range of isolates, such as those recovered from carriage screening, environments, animals, and other health-related samples from non-clinical settings.\u003c/p\u003e"},{"header":"Abbreviations","content":"\u003cp\u003eAMR\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;Antimicrobial resistance\u003c/p\u003e\n\u003cp\u003eBRC\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Biomedical Research Centre\u003c/p\u003e\n\u003cp\u003eDSM\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;Deutsche Sammlung von Mikroorganismen\u003c/p\u003e\n\u003cp\u003eEUCAST\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;European Committee on Antimicrobial Susceptibility Testing\u003c/p\u003e\n\u003cp\u003eHPRU\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;Health Protection Research Unit\u003c/p\u003e\n\u003cp\u003eLOS\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Late-onset sepsis\u003c/p\u003e\n\u003cp\u003eNCBI\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;National Center for Biotechnology Information\u003c/p\u003e\n\u003cp\u003eNICU\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Neonatal intensive care unit\u003c/p\u003e\n\u003cp\u003eNIHR\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;National Institute for Health Research\u003c/p\u003e\n\u003cp\u003eONT\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Oxford Nanopore Technologies\u003c/p\u003e\n\u003cp\u003eWGS\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;Whole-genome sequencing\u003c/p\u003e\n\u003cp\u003eUKHSA \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;UK Health Security Agency\u003c/p\u003e"},{"header":"Declarations","content":"\u003ch2\u003eEthics approval and consent to participate\u003c/h2\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003ch2\u003eConsent for publication\u003c/h2\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003ch2\u003eAvailability of data and materials\u003c/h2\u003e\n\u003cp\u003eData generated in this study are listed in Table 1. Specifically, sequence data and antibiograms have been deposited in NCBI databases under the BioProject accession PRJNA1032276. Antibiograms are accessible in BioSample records of the isolates.\u003c/p\u003e\n\u003ch2\u003eCompeting interests\u003c/h2\u003e\n\u003cp\u003eThe authors declare no completing interests.\u003c/p\u003e\n\u003ch2\u003eFunding\u003c/h2\u003e\n\u003cp\u003eThis work was mainly funded by the UKHSA and partially funded by the Wellcome Trust and Imperial College London through Y. Wan\u0026rsquo;s Imperial Institutional Strategic Support Fund Springboard Research Fellowship (grant number: PSN109). Y. Wan is a David Price Evans Research Fellow in Global Health and Infectious Diseases, funded by the University of Liverpool. Professor A. H. Holmes is a National Institute for Health and Care Research (NIHR) Senior Investigator and is affiliated with the Department of Health and Social Care funded Centre for Antimicrobial Optimisation at Imperial College London. Y. Wan, D. Meunier, M. Getino, E. Jauneikaite, A. H. Holmes, C. S. Brown, A. Demirjian, K. L. Hopkins, and B. Pichon are affiliated with the National Institute for Health and Care Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London in partnership with the UKHSA, in collaboration with, Imperial Healthcare Partners, University of Cambridge and University of Warwick (grant number: NIHR200876). The views expressed in this article are those of the authors and not necessarily those of the NHS, the National Institute for Health Research, or the Department of Health and Social Care.\u003c/p\u003e\n\u003ch2\u003eAuthors\u0026rsquo; contributions\u003c/h2\u003e\n\u003cp\u003eConceptualisation: Y. Wan, B. Pichon; resources: B. Pichon, K. L. Hopkins, J. Coelho, E. Jauneikaite, K. Moganeradj; investigation: Y. Wan, R. Pike, A. Harley, Z. Mumin, I. Potterill, D. Meunier, M. Ganner, M. Getino, K. L. Hopkins; supervision: B. Pichon, K. L. Hopkins, J. Coelho, A. Demirjian, C. S. Brown, A. H. Holmes, E. Jauneikaite, K. Moganeradj; funding acquisition: C. S. Brown, Y. Wan, A. H. Holmes, E. Jauneikaite. Writing, first draft: Y. Wan; editing: Y. Wan, D. Meunier, R. Pike, E. Jauneikaite, A. Demirjian, C. S. Brown, B. Pichon, K. L. Hopkins, K. Moganeradj, M. Ganner; approval of the final manuscript: All.\u003c/p\u003e\n\u003ch2\u003eAcknowledgements\u003c/h2\u003e\n\u003cp\u003eAll authors thank microbiology laboratories and clinicians across the UK for sharing \u003cem\u003eS. capitis\u003c/em\u003e isolates and specimen information. Illumina WGS of isolates in Batch 1 was carried out by the Colindale Sequencing Laboratory at the UKHSA. Part of the microbiological work, sample preparation, ONT sequencing, and bioinformatics analysis was undertaken at the Colebrook Laboratory, a facility supported by the NIHR Imperial Biomedical Research Centre (BRC). Part of bioinformatics analysis was performed on equipment purchased as part of MRC CARP fellowship award MR/T005254/1.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eKloos WE, Schleifer KH. Isolation and Characterization of Staphylococci from Human Skin II. Descriptions of Four New Species: \u003cem\u003eStaphylococcus warneri\u003c/em\u003e, \u003cem\u003eStaphylococcus capitis\u003c/em\u003e, \u003cem\u003eStaphylococcus hominis\u003c/em\u003e, and \u003cem\u003eStaphylococcus simulans\u003c/em\u003e 1. International Journal of Systematic and Evolutionary Microbiology. 1975;25:62\u0026ndash;79.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBannerman TL, Kloos WE. \u003cem\u003eStaphylococcus capitis\u003c/em\u003e subsp. \u003cem\u003eureolyticus\u003c/em\u003e subsp. nov. from Human Skin. 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Figure S1, genetic relatedness between the 22 selected isolates within the context of 838 isolates previously analysed. 2024. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.26048464\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.26048464\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWan Y, Ganner M, Pike R, Mumin Z, Potterill I, Meunier D et al. Table S1, sources and data accessions of \u003cem\u003eS. capitis\u003c/em\u003e isolates. 2024. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.26049013\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.26049013\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWan Y, Ganner M, Pike R, Mumin Z, Potterill I, Meunier D et al. Table S2, methods and summary statistics of genome assemblies. 2024. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.26049070\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.26049070\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWan Y, Ganner M, Pike R, Mumin Z, Potterill I, Meunier D et al. Table S3, antibiograms of isolates. 2024. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.26049094\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.26049094\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWan Y, Ganner M, Pike R, Mumin Z, Potterill I, Meunier D et al. \u003cem\u003eStaphylococcus capitis\u003c/em\u003e reference genomes. 2024. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.ncbi.nlm.nih.gov/bioproject/PRJNA1032276\u003c/span\u003e\u003cspan address=\"https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1032276\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChindelevitch L, van Dongen M, Graz H, Pedrotta A, Suresh A, Uplekar S, et al. Ten simple rules for the sharing of bacterial genotype\u0026mdash;Phenotype data on antimicrobial resistance. PLoS Comput Biol. 2023;19:e1011129.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-genomic-data","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gtic","sideBox":"Learn more about [BMC Genomic Data](http://bmcgenet.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gtic/default.aspx","title":"BMC Genomic Data","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Staphylococcus capitis, reference genomes, hybrid genome assembly, antimicrobial susceptibility, antimicrobial resistance, antibiograms, bioresource, genomics, NRCS-A clone, Nanopore MinION sequencing","lastPublishedDoi":"10.21203/rs.3.rs-4808318/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4808318/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eObjective\u003c/h2\u003e \u003cp\u003e \u003cem\u003eStaphylococcus capitis\u003c/em\u003e is part of the human microbiome and an opportunistic pathogen known to cause catheter-associated bacteraemia, prosthetic joint infections, skin and wound infections, among others. Detection of \u003cem\u003eS. capitis\u003c/em\u003e in normally sterile body sites saw an increase over the last decade in England, where a multidrug-resistant clone, NRCS-A, was widely identified in blood samples from infants in neonatal intensive care units. To address a lack of complete genomes and antibiograms of \u003cem\u003eS. capitis\u003c/em\u003e in public databases, we performed long- and short-read whole-genome sequencing, hybrid genome assembly, and antimicrobial susceptibility testing of 22 diverse isolates.\u003c/p\u003e\u003ch2\u003eData description\u003c/h2\u003e \u003cp\u003eWe present complete genome assemblies of two \u003cem\u003eS. capitis\u003c/em\u003e type strains (subspecies \u003cem\u003ecapitis\u003c/em\u003e: DSM 20326; subspecies \u003cem\u003eurealyticus\u003c/em\u003e: DSM 6717) and 20 clinical isolates (NRCS-A: 10) from England. Each genome is accompanied by minimum inhibitory concentrations of 13 antimicrobials including vancomycin, teicoplanin, daptomycin, linezolid, and clindamycin. These 22 genomes were 2.4\u0026ndash;2.7 Mbp in length and had a GC content of 33%. Plasmids were identified in 20 isolates. Resistance to teicoplanin, daptomycin, gentamicin, fusidic acid, rifampicin, ciprofloxacin, clindamycin, and erythromycin was seen in 1\u0026ndash;10 isolates. Our data are a resource for future studies on genomics, evolution, and antimicrobial resistance of \u003cem\u003eS. capitis\u003c/em\u003e.\u003c/p\u003e","manuscriptTitle":"Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-08-27 19:37:44","doi":"10.21203/rs.3.rs-4808318/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2024-10-17T13:50:07+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-10-16T23:23:15+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"37029673314068956079090438843819286573","date":"2024-10-02T14:58:35+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-08-23T15:37:23+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"36398391589869338990497233400431490784","date":"2024-08-21T12:51:04+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2024-08-20T10:34:28+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2024-07-31T06:45:34+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2024-07-31T06:45:20+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomic Data","date":"2024-07-26T13:13:14+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomic-data","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gtic","sideBox":"Learn more about [BMC Genomic Data](http://bmcgenet.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gtic/default.aspx","title":"BMC Genomic Data","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"ca75684a-d52e-46b1-9f0e-7ecac562ac88","owner":[],"postedDate":"August 27th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-02-17T16:00:19+00:00","versionOfRecord":{"articleIdentity":"rs-4808318","link":"https://doi.org/10.1186/s12863-025-01303-8","journal":{"identity":"bmc-genomic-data","isVorOnly":false,"title":"BMC Genomic Data"},"publishedOn":"2025-02-15 15:57:18","publishedOnDateReadable":"February 15th, 2025"},"versionCreatedAt":"2024-08-27 19:37:44","video":"","vorDoi":"10.1186/s12863-025-01303-8","vorDoiUrl":"https://doi.org/10.1186/s12863-025-01303-8","workflowStages":[]},"version":"v1","identity":"rs-4808318","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4808318","identity":"rs-4808318","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}