Comparative genomic epidemiology of serotype 3 IPD and carriage isolates from Southampton, UK between 2005 and 2017
Comparative genomic epidemiology of serotype 3 IPD and carriage isolates from Southampton, UK between 2005 and 2017
Serotype 3 pneumococci remains a significant cause of disease despite its inclusion in PCV13. Whilst clonal complex 180 (CC180) represents the major clone, recent studies have refined the population structure into three clades: Iα, Iβ and II, with the last being a recent divergent and more antibiotic-resistant. We present a genomic analysis of serotype 3 isolates from pae-diatric carriage and all-age invasive disease, collected between 2005 and 2017 in Southampton, UK. Forty-one isolates were available for analysis. Eighteen were isolated during the annual cross-sectional surveillance of paediatric pneumococcal car-riage. The remaining 23 were isolated from blood/cerebrospinal fluid specimens at the University Hospital Southampton NHS Foundation Trust laboratory. All carriage isolates were CC180 GPSC12. Greater diversity was seen with invasive pneumococcal disease (IPD) with three GPSC83 (ST1377: n=2, ST260: n=1) and one GPSC3 (ST1716). For both carriage and IPD, Clade Iα was dominant (94.4 and 73.9 % respectively). Two isolates were Clade II with one from carriage (a 34-month-old, October 2017) and one invasive isolate (49-year-old, August 2015). Four IPD isolates were outside the CC180 clade. All isolates were genotypically susceptible to penicillin, erythromycin, tetracycline, co-trimoxazole and chloramphenicol. Two isolates (one each from carriage and IPD; both CC180 GPSC12) were phenotypically resistant to erythromycin and tetracycline; the IPD isolate was also resistant to oxacillin.In the Southampton area, carriage and invasive disease associated with serotype 3 is predominantly caused by Clade Iα CC180 GPSC12.
IPD, Streptococcus pneumoniae, carriage, invasive pneumococcal disease, serotype 3
Cleary, David
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Lo, Stephanie W.
433b30a3-b0b1-4605-8c8a-e26b0c1c3851
Kumar, Narender
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Bentley, Stephen D.
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Faust, Saul N.
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Clarke, Stuart C.
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3 March 2023
Cleary, David
f4079c6d-d54b-4108-b346-b0069035bec0
Lo, Stephanie W.
433b30a3-b0b1-4605-8c8a-e26b0c1c3851
Kumar, Narender
af9059ae-843e-4e10-a3be-89ad16a12e54
Bentley, Stephen D.
5122ce60-0055-471f-9a77-db0b650c5ee8
Faust, Saul N.
f97df780-9f9b-418e-b349-7adf63e150c1
Clarke, Stuart C.
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17
Cleary, David, Lo, Stephanie W., Kumar, Narender, Bentley, Stephen D., Faust, Saul N. and Clarke, Stuart C.
(2023)
Comparative genomic epidemiology of serotype 3 IPD and carriage isolates from Southampton, UK between 2005 and 2017.
Microbial Genomics, 9 (3), [000945].
(doi:10.1099/mgen.0.000945).
Abstract
Serotype 3 pneumococci remains a significant cause of disease despite its inclusion in PCV13. Whilst clonal complex 180 (CC180) represents the major clone, recent studies have refined the population structure into three clades: Iα, Iβ and II, with the last being a recent divergent and more antibiotic-resistant. We present a genomic analysis of serotype 3 isolates from pae-diatric carriage and all-age invasive disease, collected between 2005 and 2017 in Southampton, UK. Forty-one isolates were available for analysis. Eighteen were isolated during the annual cross-sectional surveillance of paediatric pneumococcal car-riage. The remaining 23 were isolated from blood/cerebrospinal fluid specimens at the University Hospital Southampton NHS Foundation Trust laboratory. All carriage isolates were CC180 GPSC12. Greater diversity was seen with invasive pneumococcal disease (IPD) with three GPSC83 (ST1377: n=2, ST260: n=1) and one GPSC3 (ST1716). For both carriage and IPD, Clade Iα was dominant (94.4 and 73.9 % respectively). Two isolates were Clade II with one from carriage (a 34-month-old, October 2017) and one invasive isolate (49-year-old, August 2015). Four IPD isolates were outside the CC180 clade. All isolates were genotypically susceptible to penicillin, erythromycin, tetracycline, co-trimoxazole and chloramphenicol. Two isolates (one each from carriage and IPD; both CC180 GPSC12) were phenotypically resistant to erythromycin and tetracycline; the IPD isolate was also resistant to oxacillin.In the Southampton area, carriage and invasive disease associated with serotype 3 is predominantly caused by Clade Iα CC180 GPSC12.
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20210929_serotype3_clean
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Accepted/In Press date: 19 December 2022
Published date: 3 March 2023
Additional Information:
Funding Information:
This work was supported by Pfizer as an investigator-led research grant. Funding for whole genome sequencing was provided by the Wellcome Sanger Institute.
Funding Information:
D.W.C. was a post-doctoral researcher on GSK-funded projects in 2014/15, and currently receives grant support from Pfizer and the National Institute for Health via the NIHR Southampton Biomedical Research Centre. S.N.F. is an NIHR Senior Investigator and receives support from the National Institute for Health Research funding via the NIHR Southampton Wellcome Trust Clinical Research Facility and the NIHR Southampton Biomedical Research Centre. S.N.F. and S.C.C. act as principal investigators for clinical trials and other studies conducted on behalf of University Hospital Southampton NHS Foundation Trust/University of Southampton that are sponsored by vaccine manufacturers. No personal payments are received from them. S.N.F. and S.C.C. have participated in advisory boards for vaccine manufacturers including Pfizer but receive no personal payments for this work. D.W.C., S.N.F. and S.C.C. have received financial assistance from vaccine manufacturers to attend conferences. All grants and honoraria are paid into accounts within the respective NHS Trusts or Universities, or to independent charities. All other authors have no conflicts of interest.
Publisher Copyright:
© 2023 The Authors.
Keywords:
IPD, Streptococcus pneumoniae, carriage, invasive pneumococcal disease, serotype 3
Identifiers
Local EPrints ID: 473933
URI: http://eprints.soton.ac.uk/id/eprint/473933
ISSN: 2057-5858
PURE UUID: 20e2227f-a7f1-4d6e-9e00-5ad7cf2604a6
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Date deposited: 06 Feb 2023 17:31
Last modified: 17 Mar 2024 03:35
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Contributors
Author:
Stephanie W. Lo
Author:
Narender Kumar
Author:
Stephen D. Bentley
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