Whole-genome sequencing reveals widespread presence of Staphylococcus capitis NRCS-A clone in neonatal units across the United Kingdom - 05/08/23

Doi : 10.1016/j.jinf.2023.06.020

Yu Wan ^a,^b,^⁎ , Mark Ganner ^c, Zaynab Mumin ^c, Derren Ready ^d,^e, Ginny Moore ^f, Isabelle Potterill ^c, Karthik Paranthaman ^g, Elita Jauneikaite ^b,^h,ⁱ, Bharat Patel ^j, Alessandra Harley ^c, Maria Getino ^b,
UKHSA S. capitis Incident Management Team^¹
See Appendix A for team members not listed in the author list above.
Colin S. Brown ^a,^b, Alicia Demirjian ^a,^b,^k,^l,^{^{2
Bruno Pichon and Alicia Demirjian contributed equally to this manuscript.}}, Bruno Pichon ^a,^b,^{^{2
Bruno Pichon and Alicia Demirjian contributed equally to this manuscript.}}
^a HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
^b NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
^c Reference Services Division, National Infection Service, UK Health Security Agency, London, UK
^d UK Health Security Agency, Field Service South West, Bristol, UK
^e NIHR Health Protection Research Unit in Behavioural Science and Evaluation at University of Bristol, Bristol, UK
^f Research and Evaluation, UK Health Security Agency, Porton Down, Salisbury, UK
^g Field Service, UK Health Security Agency, London, UK
^h Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
ⁱ MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
^j Public Health Laboratory London, Science Group, UK Health Security Agency, London, UK
^k Paediatric Infectious Diseases and Immunology, Evelina London Children’s Hospital, London, UK
^l Faculty of Life Sciences & Medicine, King’s College London, London, UK

^⁎Corresponding author at: HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK.HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security AgencyLondonUK

Summary

Objective

Increased incidence of neonatal Staphylococcus capitis bacteraemia in summer 2020, London, raised suspicion of widespread multidrug-resistant clone NRCS-A. We set out to investigate the molecular epidemiology of this clone in neonatal units (NNUs) across the UK.

Methods

We conducted whole-genome sequencing (WGS) on presumptive S. capitis NRCS-A isolates collected from infants admitted to nationwide NNUs and from environmental sampling in two distinct NNUs in 2021. Previously published S. capitis genomes were added for comparison. Genetic clusters of NRCS-A isolates were defined based on core-genome single-nucleotide polymorphisms.

Results

We analysed WGS data of 838 S. capitis isolates and identified 750 NRCS-A isolates. We discovered a possible UK-specific NRCS-A lineage consisting of 611 isolates collected between 2005 and 2021. We determined 28 genetic clusters of NRCS-A isolates, which covered all geographical regions in the UK, and isolates of 19 genetic clusters were found in ≥2 regions, suggesting inter-regional spread. Within the NRCS-A clone, strong genetic relatedness was identified between contemporary clinical and incubator-associated fomite isolates and between clinical isolates associated with inter-hospital infant transfer.

Conclusions

This WGS-based study confirms the dispersion of S. capitis NRCS-A clone amongst NNUs across the UK and urges research on improving clinical management of neonatal S. capitis infection.

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Graphical Abstract

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Highlights

•	Whole-genome sequencing of 760 Staphylococcus capitis isolates from across the UK.
•	Widespread presence of the S. capitis NRCS-A clone in neonatal units across the UK.
•	Twenty-eight genetic clusters of NRCS-A isolates covered all UK geographic regions.
•	Strong genetic links between clinical and fomite NRCS-A isolates in a neonatal unit.
•	Inter-hospital genetic links between NRCS-A isolates associated with infant transfer.

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Keywords : Staphylococcus capitis, NRCS-A clone, Whole-genome sequencing, Neonatal units, Bacteraemia, Molecular epidemiology, Population structure, Phylogenetics

Plan

Introduction

Materials and methods

Isolate collection

Whole-genome sequencing

Genetic, geographical, and specimen diversities of S. capitis isolates

Geographical distribution of NRCS-A isolates

Genetic diversity of NRCS-A isolates from the same patients

Genetic links between clinical and fomite NRCS-A isolates in a NICU

Inter-hospital genetic links between NRCS-A isolates

Discussion

Funding

Export

Vol 87 - N° 3

P. 210-219 - septembre 2023 Retour au numéro

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Whole-genome sequencing reveals widespread presence of Staphylococcus capitis NRCS-A clone in neonatal units across the United Kingdom - 05/08/23

Summary

Objective

Methods

Results

Conclusions

Graphical Abstract

Highlights

Plan

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