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Emergence of Dominant Toxigenic M1T1 Streptococcus Pyogenes Clone During Increased Scarlet Fever Activity in England: A Population-Based Molecular Epidemiological Study

57 Pages Posted: 28 Apr 2019

See all articles by Nicola N. Lynskey

Nicola N. Lynskey

Imperial College London - Department of Medicine; Imperial College London - MRC Centre for Molecular Bacteriology & Infection

Elita Jauneikaite

Imperial College London - Section of Infectious Diseases and Immunity

Ho Kwong Li

Imperial College London - Section of Infectious Diseases and Immunity

Xiangyun Zhi

Imperial College London - Section of Infectious Diseases and Immunity

Claire E. Turner

Imperial College London - Department of Medicine; University of Sheffield - Department of Molecular Biology and Biotechnology

Mia Mosavie

Imperial College London - Section of Infectious Diseases and Immunity

Max Pearson

Imperial College London - Section of Infectious Diseases and Immunity; Imperial College London - Department of Medicine; Imperial College London - MRC Centre for Molecular Bacteriology & Infection

Masanori Asai

Imperial College London - Section of Infectious Diseases and Immunity

Ludmila Lobkowicz

Imperial College London - Section of Infectious Diseases and Immunity

J. Yimmy Chow

Imperial College London - NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance

Julian Parkhill

Imperial College London - NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance

Theresa Lamagni

Government of the United Kingdom, Department of Health and Social Care, National Infection Service, Healthcare-Associated Infection and Antimicrobial Resistance (HCAI & AMR) Division

Victoria J. Chalker

Imperial College London - NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance

Shiranee Sriskandan

Imperial College London - Department of Medicine; Imperial College London - MRC Centre for Molecular Bacteriology & Infection; Imperial College London - NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance

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Abstract

Background:  England is experiencing scarlet fever activity unprecedented in modern times. In 2016, England's scarlet fever seasonal rise coincided with an unexpected elevation in invasive Streptococcus pyogenes infections. We describe the molecular-epidemiological investigation of these events and emergence of a new emm1 lineage.    

Methods: We analysed changes in S. pyogenes emm-genotypes, and notifications of scarlet fever and invasive disease 2014-2016 using regional and national data. We analysed genomes of 135 non-invasive and 552 invasive emm1 isolates from 2009-2016, and compared 2800 global emm1 sequences. Expression of Streptococcal pyrogenic exotoxin (Spe)A by sequenced non-invasive emm1 isolates was quantified.    

Findings: Coincident with national increases in scarlet fever and invasive disease, emm1 S. pyogenes infections increased significantly, accounting for 32·6% (47/144) of pharyngeal isolates in North West London and 41·9% (267/637) of invasive isolates nationally in March-May 2016. Sequences of emm1 isolates from 2009-2016 demonstrated emergence of a new emm1 lineage (M1UK), with overlap of pharyngitis, scarlet fever, and invasive M1UK strains, that could be genotypically distinguished from pandemic emm1 isolates (M1global). Compared with M1global , median expression of SpeA increased 9-fold in M1UK isolates. M1UK expanded nationally to represent 84% (252/299) of all emm1, genomes in 2016; analysis identified two M1UK isolates outside the UK.

Interpretation: A dominant new emm1 S. pyogenes lineage characterized by increased SpeA production has emerged during increased S. pyogenes activity in England. The expanded reservoir of M1UK and recognised invasive potential of emm1 S. pyogenes provide plausible explanation for increased invasive disease, and rationale for global surveillance.

Funding Statement: Supported by grants from Medical Research Council (MR/P022669/1); NIHR Health Protection Unit in AMR and HCAI (HPRU-2012-10047); NIHR BRC SpyVAC; Conor Kerin Foundation. NNL is a Sir Henry Wellcome Postdoctoral Research Fellow funded by the Wellcome Trust (103197/Z/13/Z); EJ is a Rosetrees/Stoneygate 2017 Imperial College Research Fellow (M683).

Declaration of Interests: JP is a consultant to Next Gen Diagnostics LLC; other authors declare no interests.

Ethics Approval Statement: Clinical data were linked to isolates and anonymized in accordance with Research Ethics approval 06/Q0406/20.

Keywords: Streptococcus pyogenes, genome, Scarlet Fever, Tonsillitis, Invasive infection, Sepsis, Superantigen, SpeA

Suggested Citation

Lynskey, Nicola N. and Jauneikaite, Elita and Kwong Li, Ho and Zhi, Xiangyun and Turner, Claire E. and Mosavie, Mia and Pearson, Max and Asai, Masanori and Lobkowicz, Ludmila and Chow, J. Yimmy and Parkhill, Julian and Lamagni, Theresa and Chalker, Victoria J. and Sriskandan, Shiranee, Emergence of Dominant Toxigenic M1T1 Streptococcus Pyogenes Clone During Increased Scarlet Fever Activity in England: A Population-Based Molecular Epidemiological Study (April 24, 2019). Available at SSRN: https://ssrn.com/abstract=3377544

Nicola N. Lynskey

Imperial College London - Department of Medicine

South Kensington Campus
Exhibition Road
London, Greater London SW7 2AZ
United Kingdom

Imperial College London - MRC Centre for Molecular Bacteriology & Infection

London
United Kingdom

Elita Jauneikaite

Imperial College London - Section of Infectious Diseases and Immunity

London
United Kingdom

Ho Kwong Li

Imperial College London - Section of Infectious Diseases and Immunity

London
United Kingdom

Xiangyun Zhi

Imperial College London - Section of Infectious Diseases and Immunity

London
United Kingdom

Claire E. Turner

Imperial College London - Department of Medicine

South Kensington Campus
Exhibition Road
London, Greater London SW7 2AZ
United Kingdom

University of Sheffield - Department of Molecular Biology and Biotechnology

United Kingdom

Mia Mosavie

Imperial College London - Section of Infectious Diseases and Immunity

London
United Kingdom

Max Pearson

Imperial College London - Section of Infectious Diseases and Immunity

London
United Kingdom

Imperial College London - Department of Medicine

South Kensington Campus
Exhibition Road
London, Greater London SW7 2AZ
United Kingdom

Imperial College London - MRC Centre for Molecular Bacteriology & Infection

London
United Kingdom

Masanori Asai

Imperial College London - Section of Infectious Diseases and Immunity

London
United Kingdom

Ludmila Lobkowicz

Imperial College London - Section of Infectious Diseases and Immunity

London
United Kingdom

J. Yimmy Chow

Imperial College London - NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance

London
United Kingdom

Julian Parkhill

Imperial College London - NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance

London
United Kingdom

Theresa Lamagni

Government of the United Kingdom, Department of Health and Social Care, National Infection Service, Healthcare-Associated Infection and Antimicrobial Resistance (HCAI & AMR) Division

United Kingdom

Victoria J. Chalker

Imperial College London - NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance

London
United Kingdom

Shiranee Sriskandan (Contact Author)

Imperial College London - Department of Medicine ( email )

South Kensington Campus
Exhibition Road
London, Greater London SW7 2AZ
United Kingdom

Imperial College London - MRC Centre for Molecular Bacteriology & Infection ( email )

London
United Kingdom

Imperial College London - NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance ( email )

London
United Kingdom

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