ABSTRACT The multidrug-resistant _Staphylococcus capitis_ NRCS-A clone is responsible for sepsis in preterm infants in neonatal intensive care units (NICUs) worldwide. Here, to retrace the

spread of this clone and to identify drivers of its specific success, we investigated a representative collection of 250 _S. capitis_ isolates from adults and newborns. Bayesian analyses

confirmed the spread of the NRCS-A clone and enabled us to date its emergence in the late 1960s and its expansion during the 1980s, coinciding with the establishment of NICUs and the

increasing use of vancomycin in these units, respectively. This dynamic was accompanied by the acquisition of mutations in antimicrobial resistance- and bacteriocin-encoding genes.

NICU-associated pathogens. These findings illustrate how the broad use of antibiotics can repeatedly lead initially commensal drug-susceptible bacteria to evolve into multidrug-resistant

clones that are able to successfully spread worldwide and become pathogenic for highly vulnerable patients. Access through your institution Buy or subscribe This is a preview of subscription

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* Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS _STAPHYLOCOCCUS AUREUS_ ST764-SCC_MEC_II HIGH-RISK CLONE

IN BLOODSTREAM INFECTIONS REVEALED THROUGH NATIONAL GENOMIC SURVEILLANCE INTEGRATING CLINICAL DATA Article Open access 19 March 2025 RAPID METHICILLIN RESISTANCE DIVERSIFICATION IN

_STAPHYLOCOCCUS EPIDERMIDIS_ COLONIZING HUMAN NEONATES Article Open access 18 October 2021 DEMOGRAPHIC FLUCTUATIONS IN BLOODSTREAM _STAPHYLOCOCCUS AUREUS_ LINEAGES CONFIGURE THE MOBILE GENE

POOL AND ANTIMICROBIAL RESISTANCE Article Open access 07 May 2024 DATA AVAILABILITY The datasets supporting the results of this article are available from the Sequence Read Archive under

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ACKNOWLEDGEMENTS We thank M. Stegger and his team for insightful exchanges during the manuscript drafting and C. Allix-Béguec, C. Gaudin, M. Mairey and S. Duthoy for their help in genome

sequencing. This project was supported by the European Society of Clinical Microbiology and Infectious Diseases study group (Project P307-14), the Fondation pour la Recherche Médicale

(project ING20160435683) and the European Union Patho-Ngen-Trace (project FP7-278864). AUTHOR INFORMATION Author notes * These authors contributed equally: Marine Butin, Frédéric Laurent.

AUTHORS AND AFFILIATIONS * Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, Université des Antilles, EPHE, Paris, France

Thierry Wirth, Jean-Philippe Rasigade & Maxime Barbier * PSL University, EPHE, Paris, France Thierry Wirth * Institut des Agents Infectieux, Département de Bactériologie, Centre

National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France Marine Bergot, Jean-Philippe Rasigade, Patricia Martins-Simoes & Frédéric Laurent * Centre International

de recherche en Infectiologie, INSERM U1111 - CNRS UMR5308 - ENS Lyon - Université Lyon 1, Lyon, France Jean-Philippe Rasigade, Patricia Martins-Simoes, Marine Butin, Frédéric Laurent, 

Francois Vandenesch & Francois Vandenesch * Staphylococcus Reference Section, National Infection Service, Public Health England, London, UK Bruno Pichon, Rachel Pike & Angela Kearns

* Laboratoire Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, Lyon, France Laurent Jacob * Institut de Biologie de la cellule (I2BC-UMR9198), CNRS, CEA, Univ. Paris Sud,

Université Paris Saclay, Gif-sur-Yvette, France Pierre Tissieres * Service de Réanimation Néonatale, Hôpitaux Universitaires Paris Sud APHP, Le Kremlin-Bicêtre, Paris, France Pierre

Tissieres * Service de Réanimation Néonatale, Hôpital Croix Rousse, Hospices Civils de Lyon, Lyon, France Jean-Charles Picaud * Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur

de Lille, U1019 - UMR 8204 - CIIL - Centre d’Infection et d’Immunité de Lille, Lille, France Philip Supply * Service de Réanimation Néonatale, Hôpital Femme Mère Enfant, Hospices Civils de

Lyon, Lyon, France Marine Butin & Olivier Claris * Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital, Prague, Czech Republic Vaclava Adamkova *

Tan Tock Seng Hospital, Singapore, Singapore Timothy Barkham * University Hospital Münster, Münster, Germany Karsten Becker * Irish Meningitis and Sepsis Reference Laboratory, Temple Street

Children’s University Hospital, Dublin, Ireland Desiree Bennett * Vanderbilt University School of Medicine, Nashville, USA Clarence Buddy Creech * Instituto de Tecnologia Quimica e

Biologica, Oeiras, Portugal Herminia De Lencastre * School of Applied Sciences, RMIT University, Bundoora, Australia Margaret Deighton * Hôpital Erasme – ULB, Bruxelles, Belgique Olivier

Denis * University of New Castle, Callaghan, Australia John Ferguson * Chang Gung Children’s Hospital, Taoyuan, Taiwan Yhu-Chering Huang * University Hospital of North Norway, Tromsø, Norway

Claus Klingenberg * Oslo University Hospital Rikshospitalet, Oslo, Norway Andre Ingebretsen * CHU Sainte-Justine, Montréal, Canada Celine Laferrière * Rio de Janeiro Federal University, Rio

de Janeiro, Brazil Katia Regina Netto dos Santos * Laboratory of Bacteriology and the Genome Research Lab, Geneva University Hospital, Geneva, Switzerland Jacques Schrenzel * University of

Patras, Patras, Greece Iris Spiliopoulou * University of Catania, Catania, Italy Stefania Stefani * Seoul National University Hospital, Seoul, Korea Kim TaekSoo * Helsinki University Central

Hospital laboratory HUSLAB, Helsinki, Finland Eveliina Tarkka * Medical Microbiology and Infection Prevention, University Medical Center, Groningen, Netherlands Alex Friedrich * Medical

Microbiology & Infection Control, Amsterdam, Netherlands Christina Vandenbroucke-Grauls * University of Otago, Otago, New Zealand James Ussher * Children Healthcare of Atlanta, Atlanta,

USA Lars Westblade * Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom Jodi Lindsay * Statens Serum Institut, Microbiology and Infection

Control, Reference Laboratory for Antimicrobial Resistance and Staphylococci, Copenhagen, Denmark Anders Rhod Larsen * Institute of Global Health, Epidemiology & Biostatistics, Ruprecht

Karls University, Heidelberg, Germany Philipp Zanger * Institut für Med. Mikrobiologie Universitätsklinikum Münster, Münster, Germany Barbara C. Kahl * Hospital Universitari Germans Trias i

Pujol, Microbiology, Badalona, Spain Cristina Prat Aymerich Authors * Thierry Wirth View author publications You can also search for this author inPubMed Google Scholar * Marine Bergot View

author publications You can also search for this author inPubMed Google Scholar * Jean-Philippe Rasigade View author publications You can also search for this author inPubMed Google Scholar

* Bruno Pichon View author publications You can also search for this author inPubMed Google Scholar * Maxime Barbier View author publications You can also search for this author inPubMed 

Google Scholar * Patricia Martins-Simoes View author publications You can also search for this author inPubMed Google Scholar * Laurent Jacob View author publications You can also search for

this author inPubMed Google Scholar * Rachel Pike View author publications You can also search for this author inPubMed Google Scholar * Pierre Tissieres View author publications You can

also search for this author inPubMed Google Scholar * Jean-Charles Picaud View author publications You can also search for this author inPubMed Google Scholar * Angela Kearns View author

publications You can also search for this author inPubMed Google Scholar * Philip Supply View author publications You can also search for this author inPubMed Google Scholar * Marine Butin

View author publications You can also search for this author inPubMed Google Scholar * Frédéric Laurent View author publications You can also search for this author inPubMed Google Scholar

CONSORTIA THE INTERNATIONAL CONSORTIUM FOR STAPHYLOCOCCUS CAPITIS NEONATAL SEPSIS * Vaclava Adamkova * , Timothy Barkham * , Karsten Becker * , Desiree Bennett * , Olivier Claris * , 

Clarence Buddy Creech * , Herminia De Lencastre * , Margaret Deighton * , Olivier Denis * , John Ferguson * , Yhu-Chering Huang * , Claus Klingenberg * , Andre Ingebretsen * , Celine

Laferrière * , Katia Regina Netto dos Santos * , Jacques Schrenzel * , Iris Spiliopoulou * , Stefania Stefani * , Kim TaekSoo * , Eveliina Tarkka * , Alex Friedrich * , Christina

Vandenbroucke-Grauls * , James Ussher * , Francois Vandenesch *  & Lars Westblade THE ESGS STUDY GROUP OF ESCMID * Jodi Lindsay * , Francois Vandenesch * , Anders Rhod Larsen * , Philipp

Zanger * , Barbara C. Kahl *  & Cristina Prat Aymerich CONTRIBUTIONS M.Butin, T.W., J.-C.P. and F.L. conceived the project. M.Butin and F.L. established and analysed clinical and

reference isolate datasets. B.P., A.K. and R.P. performed DNA extractions. P.S. performed DNA sequencing. B.P., A.K. and R.P. performed antimicrobial susceptibility testing. P.T. performed

phagocytosis assays. M.Butin performed all additional phenotypic assays. T.W., M.Barbier, P.M.-S. and M.Bergot analysed genomic data. J.-P.R. participated in genomic analyses and performed

THD analysis. M.Bergot and L.J. performed GWAS analysis. T.W., M.Butin, P.S. and F.L. drafted the manuscript. All authors reviewed and contributed to the final manuscript. CORRESPONDING

AUTHORS Correspondence to Thierry Wirth or Marine Butin. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer

Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. EXTENDED DATA EXTENDED DATA FIG. 1 CLONALFRAMEML ANALYSIS OF RECOMBINATION IN

_S. CAPITIS_. Analysis was based on 55 genomes: all non-NRCS-A strains were included, however the clone NRCS-A was undersampled to avoid a statistical bias in favor of mutational changes.

Dark blue horizontal bars indicate recombination events detected by the analysis. EXTENDED DATA FIG. 2 NRCS-A HOST TYPES AND GENETIC STRUCTURE. A, NRCS-A isolates within an MSTREE based on

the whole genome sequencing data. Each strain is represented by a circle or a fraction of a circle, colors correspond to different host types. Numbers indicate the mutational steps between

the strains. B, Same data as above but represented in an MDS plot. C, Within NRCS-A diversity as assessed by mean pairwise SNP distances (N=197). D, Graphical chart representing the fraction

of strains obtained from newborns in the basal, Proto-outbreak 1 and 2 and Outbreak strains. EXTENDED DATA FIG. 3 GENOME SCAN ANALYSIS OF NRCS-A STRAINS FOR DETECTING SNPS INVOLVED IN LOCAL

ADAPTATION. A, Plot of the first 2 principal components (PC). The 197 NRCS-A strains are represented by points and colorized according to their phylogenic origin (Proto-outbreak 1 and 2 in

blue, and Outbreak in red). PC 2 is the one separating the basal proto-outbreak 1 and 2 strains from the outbreak strains. B, Manhattan plot representing the 3,658 SNPs and values obtained

after performing Mahalanobis distances. The SNPs are colorized according to the PC to which they correlate most (PC1 = black, PC2 = red, PC3 = green and PC4 = blue). EXTENDED DATA FIG. 4

SPECIFIC SNPS IN OUTBREAK AND ALPHA ISOLATES. Respectively 32 and 17 SNPs were specifically identified in Outbreak strains among NRCS-A strains (n=197) or in clade Alpha strains among Basal

strains (n=53). Those SNPs were identified using PCADAPT. EXTENDED DATA FIG. 5 TERTIARY PROTEIN STRUCTURES. A, Positions on the tertiary protein structure of outbreak specific non-synonymous

mutations detected via PCADAPT and involved in antibiotic resistance (tigecycline and vancomycin). B, Positions on the tertiary protein structure of alpha-clone specific non-synonymous

mutations for a set of two genes involved in cell wall synthesis. Visualization and predictions were executed by PHYRE2 software (http://www.sbg.bio.ic.ac.uk/phyre2). EXTENDED DATA FIG. 6

PHENOTYPIC AND GENOTYPIC RESISTANCE PATTERNS OF _S. CAPITIS_ ISOLATES. Phenotypic data of _S. capitis_ isolates (n=250) were obtained from agar dilution and biomarkers of antibiotic

resistance were detected using GENEFINDER. Comparison between groups of isolates was performed using two-sided Fisher exact test. EXTENDED DATA FIG. 7 PHENOTYPIC ASSAYS COMPARING A SUBSET OF

REPRESENTATIVE ISOLATES OF EACH OF THE FOUR SUBGROUPS IDENTIFIED BY THE PHYLOGEOGRAPHICAL ANALYSIS (OUTBREAK, PROTO-OUTBREAK 1, PROTO-OUTBREAK 2 AND ‘OTHER ISOLATES’). In all 6 graphs,

center values represent means. A, Culture supernatants cytotoxicity assay using THP1 cells, adjusted on a positive control (Triton) of 12 representative _S. capitis_ isolates (two

independent experiments in triplicate for each strains). B, Survival of strains (n=12) after 24 hours of persistence in desiccation conditions (two independent experiments in triplicate for

each strains). C, Comparison of the doubling time of bacterial growth during the exponential phase in standard conditions (BHI) of 24 representative _S. capitis_ isolates (three independent

experiments in triplicate for each strains) and D, Under oxidative stress (ethanol-supplemented medium to a final concentration of 6.5%) (n=24 strains, three independent experiments in

triplicate for each strains). E, Quantification of biofilm production of 24 representative _S. capitis_ isolates using crystal violet method (expressed as optic densitometry at 590nm) (three

independent experiments in triplicate for each strains). F, Phagocytosis index of monocytes and granulocytes from cord blood for a subset of 5 representative isolates of “Outbreak” and

“Basal” isolates (four independent experiments). Of note, results of phagocytosis of neutrophils and activated neutrophils are not represented here because they were similar to those with

granulocytes. EXTENDED DATA FIG. 8 GENES ASSOCIATED WITH VANCOMYCIN MIC AND/OR THD SUCCESS INDEX USING DBGWAS. Here are represented genes with a -log10 (HMP) > 7.5 on either axis, and/or

> 5 on both axes, thus considered significant. SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION Results, including three supplementary figures. REPORTING SUMMARY SUPPLEMENTARY TABLE 1

This table includes source data and details about each isolate (identification, origin, phenotypic and genomic characteristics, genes content and THD index). RIGHTS AND PERMISSIONS Reprints

and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Wirth, T., Bergot, M., Rasigade, JP. _et al._ Niche specialization and spread of _Staphylococcus capitis_ involved in neonatal sepsis.

_Nat Microbiol_ 5, 735–745 (2020). https://doi.org/10.1038/s41564-020-0676-2 Download citation * Received: 19 October 2019 * Accepted: 28 January 2020 * Published: 27 April 2020 * Issue

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