TY - JOUR
T1 - The ongoing Streptococcus pyogenes (Group A Streptococcus) outbreak in London, United Kingdom in December 2022: a molecular epidemiology study.
AU - Alcolea-Medina, Adela
AU - Snell, Luke Blagdon
AU - Alder, Christopher
AU - Charalampous, Themoula
AU - Williams, Tom G.S.
AU - Tan, Mark
AU - Al-Yaakoubi, Noor
AU - Humayun, Gul
AU - Newsholme , William
AU - Goldenberg, Simon
AU - Nebbia, Gaia
AU - Neil, Stuart
AU - Batra, Rahul
AU - Edgeworth, Jonathan
N1 - Funding Information:
The work was funded by the Medical Research Council (LBS: MR/W025140/1, GN: MR/T005416/1, JDE, AA-M, RB, GN , LBS , TC: MC_PC_19,041). JDE has received funding from the Guy's and St. Thomas' Charity (TR130505). AA-M and members of the Synnovis Microbiology Laboratory Group are full-time employees of Synnovis. JDE holds a part-time employment contract with Oxford Nanopore Technologies that commenced in October 2022. Guy's & St Thomas' NHS Foundation Trust signed a commercial collaboration agreement with Oxford Nanopore Technology in September 2022. WN, CA, GH, MT, NA-Y, SDJN, SG and TGSW have no conflicts of interest to declare.
Funding Information:
The work was funded by the Medical Research Council (LBS: MR/W025140/1, GN: MR/T005416/1, JDE, AA-M, RB, GN, LBS, TC: MC_PC_19,041). JDE has received funding from the Guy's and St. Thomas' Charity (TR130505). AA-M and members of the Synnovis Microbiology Laboratory Group are full-time employees of Synnovis. JDE holds a part-time employment contract with Oxford Nanopore Technologies that commenced in October 2022. Guy's & St Thomas' NHS Foundation Trust signed a commercial collaboration agreement with Oxford Nanopore Technology in September 2022. WN, CA, GH, MT, NA-Y, SDJN, SG and TGSW have no conflicts of interest to declare.AA-M, LBS, CA, TC and TGSW were involved in conceptualization, data acquisition, methodology and formal analysis. AA-M and LBS were involved in writing—original draft. The Synnovis Microbiology Laboratory Group, MT, GH and NA-Y were involved in the investigation. WN, SDJN, SG, GN and JDE were involved in supervision and writing—review and editing. RB was involved in project administration and resources. AA-M, LBS, TC, SDJN, GN, RB and JDE were involved in funding acquisition.
Publisher Copyright:
© 2023 The Authors
PY - 2023/3/15
Y1 - 2023/3/15
N2 - Objectives: Epidemiological and whole-genome sequencing analysis of an ongoing outbreak of Streptococcus pyogenes (Group A Streptococcus) in London (United Kingdom). Methods: Prospective identification of Group A Streptococcus cases from a diagnostic laboratory serving central and south London between 27 November and 10 December 2022. Case notes were reviewed and isolates were retrieved. Case numbers were compared with the previous 5 years. Whole-genome sequencing was performed with long-read, nanopore technology for emm typing and identification of superantigen genes. Associations of pathogen-related factors with an invasive disease were assessed by single-variable and multi-variable logistic regression. Results: Case numbers began increasing in October 2022 from a baseline of 2.0 cases per day, and in December 2022, the average daily case numbers reached 10.8 cases per day, four-fold the number usually seen in winter. A total of 113 cases were identified during the prospective study period. Three quarters (86/113, 76%) were paediatric cases, including 2 deaths. Of 113 cases, 11 (10%) were invasive. In total, 56 isolates were successfully sequenced, including 10 of 11 (91%) invasive isolates. The emm12 (33/56, 59%) and emm1 (9/56, 16%) types were predominant, with 7 of 9 (78%) emm1 isolates being from the M1uk clone. The majority of invasive isolates had superantigen genes spea (7/10, 70%) and spej (8/10, 80%), whereas, in non-invasive isolates, these superantigen genes were found less frequently (spea: 5/46, 11% and spej: 7/46, 15%). By multivariable analysis of pathogen-related factors, spea (OR 8.9, CI 1.4–57, p 0.020) and spej (OR 12, CI 1.8–78, p 0.011) were associated with invasive disease. Conclusions: emm12 and emm1 types predominate in the ongoing outbreak, which mainly affects children. In this outbreak, the spea and spej superantigen genes are associated with the severity of presentation.
AB - Objectives: Epidemiological and whole-genome sequencing analysis of an ongoing outbreak of Streptococcus pyogenes (Group A Streptococcus) in London (United Kingdom). Methods: Prospective identification of Group A Streptococcus cases from a diagnostic laboratory serving central and south London between 27 November and 10 December 2022. Case notes were reviewed and isolates were retrieved. Case numbers were compared with the previous 5 years. Whole-genome sequencing was performed with long-read, nanopore technology for emm typing and identification of superantigen genes. Associations of pathogen-related factors with an invasive disease were assessed by single-variable and multi-variable logistic regression. Results: Case numbers began increasing in October 2022 from a baseline of 2.0 cases per day, and in December 2022, the average daily case numbers reached 10.8 cases per day, four-fold the number usually seen in winter. A total of 113 cases were identified during the prospective study period. Three quarters (86/113, 76%) were paediatric cases, including 2 deaths. Of 113 cases, 11 (10%) were invasive. In total, 56 isolates were successfully sequenced, including 10 of 11 (91%) invasive isolates. The emm12 (33/56, 59%) and emm1 (9/56, 16%) types were predominant, with 7 of 9 (78%) emm1 isolates being from the M1uk clone. The majority of invasive isolates had superantigen genes spea (7/10, 70%) and spej (8/10, 80%), whereas, in non-invasive isolates, these superantigen genes were found less frequently (spea: 5/46, 11% and spej: 7/46, 15%). By multivariable analysis of pathogen-related factors, spea (OR 8.9, CI 1.4–57, p 0.020) and spej (OR 12, CI 1.8–78, p 0.011) were associated with invasive disease. Conclusions: emm12 and emm1 types predominate in the ongoing outbreak, which mainly affects children. In this outbreak, the spea and spej superantigen genes are associated with the severity of presentation.
UR - http://www.scopus.com/inward/record.url?scp=85156192771&partnerID=8YFLogxK
U2 - https://doi.org/10.1016/j.cmi.2023.03.001
DO - https://doi.org/10.1016/j.cmi.2023.03.001
M3 - Article
SN - 1198-743X
VL - 29
SP - 887
EP - 890
JO - CLINICAL MICROBIOLOGY AND INFECTION
JF - CLINICAL MICROBIOLOGY AND INFECTION
IS - 7
ER -