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

Affiliations

¹ HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK. Electronic address: yu.wan@ukhsa.gov.uk.
² Reference Services Division, National Infection Service, UK Health Security Agency, London, UK.
³ UK Health Security Agency, Field Service South West, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation at University of Bristol, Bristol, UK.
⁴ Research and Evaluation, UK Health Security Agency, Porton Down, Salisbury, UK.
⁵ Field Service, UK Health Security Agency, London, UK.
⁶ NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK; Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
⁷ Public Health Laboratory London, Science Group, UK Health Security Agency, London, UK.
⁸ NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK.
⁹ HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK.
¹⁰ HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK; Paediatric Infectious Diseases and Immunology, Evelina London Children's Hospital, London, UK; Faculty of Life Sciences & Medicine, King's College London, London, UK.

PMID: 37394013
DOI: 10.1016/j.jinf.2023.06.020

Free article

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

Yu Wan et al. J Infect. 2023 Sep.

Free article

. 2023 Sep;87(3):210-219.

doi: 10.1016/j.jinf.2023.06.020. Epub 2023 Jun 30.

Affiliations

¹ HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK. Electronic address: yu.wan@ukhsa.gov.uk.
² Reference Services Division, National Infection Service, UK Health Security Agency, London, UK.
³ UK Health Security Agency, Field Service South West, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation at University of Bristol, Bristol, UK.
⁴ Research and Evaluation, UK Health Security Agency, Porton Down, Salisbury, UK.
⁵ Field Service, UK Health Security Agency, London, UK.
⁶ NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK; Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
⁷ Public Health Laboratory London, Science Group, UK Health Security Agency, London, UK.
⁸ NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK.
⁹ HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK.
¹⁰ HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK; Paediatric Infectious Diseases and Immunology, Evelina London Children's Hospital, London, UK; Faculty of Life Sciences & Medicine, King's College London, London, UK.

PMID: 37394013
DOI: 10.1016/j.jinf.2023.06.020

Abstract

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.

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

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Conflict of interest statement

Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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

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

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