1
|
Cleary DW, Lo SW, Kumar N, Bentley SD, Faust SN, Clarke SC. Comparative genomic epidemiology of serotype 3 IPD and carriage isolates from Southampton, UK between 2005 and 2017. Microb Genom 2023; 9. [PMID: 36867094 PMCID: PMC10132069 DOI: 10.1099/mgen.0.000945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
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 paediatric 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 carriage. 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.
Collapse
Affiliation(s)
- David W Cleary
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK.,Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Narender Kumar
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | | | - Saul N Faust
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK.,Southampton Clinical Research Facility, University Hospital Southampton Foundation NHS Trust, Southampton, UK
| | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK.,Global Health Research Institute, University of Southampton, Southampton, UK
| |
Collapse
|
2
|
Lister AJJ, Le CF, Cheah ESG, Desa MNM, Cleary DW, Clarke SC. Serotype distribution of invasive, non-invasive and carried Streptococcus pneumoniae in Malaysia: a meta-analysis. Pneumonia (Nathan) 2021; 13:9. [PMID: 34030731 PMCID: PMC8147341 DOI: 10.1186/s41479-021-00086-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Background Pneumococcal pneumonia is the leading cause of under-five mortality globally. The surveillance of pneumococcal serotypes is therefore vital for informing pneumococcal vaccination policy and programmes. Pneumococcal conjugate vaccines (PCVs) have been available as an option in the private healthcare setting and beginning December 2020, PCV10 was incorporated as part of routine national immunisation programme (NIP) in Malaysia. We searched existing literature on pneumococcal serotype distribution across Malaysia to provide an overall view of this distribution before the implementation of PCV10. Methods Online databases (PubMed, Ovid MEDLINE and Scopus), reference lists of articles identified, and grey literature (Malaysian Ministry of Health website, WHO website) were systematically searched for relevant literature on pneumococcal serotype distribution across Malaysia up to 10th November 2020. No lower date limit was set to maximise the number of target reports returned. Results of serotypes were split by age categories, including ≤5 years, > 5 years and unreported for those that did not specify. Results The search returned 18 relevant results, with a total of 2040 isolates. The most common serotypes across all disease types were 19F (n = 313, 15.3% [95%CI: 13.8–17.0]), 23F (n = 166, 8.1% [95%CI: 7.0–9.4]), 14 (n = 166, 8.1% [95%CI: 7.0–9.4]), 6B (n = 163, 8.0% [95%CI: 6.9–9.2]) and 19A (n = 138, 6.8% [95%CI: 5.8–7.9]). Conclusion Four of the most common serotypes across all isolate sources in Malaysia are covered by PCV10, while PCV13 provides greater serotype coverage in comparison to PCV10. There is still a need for surveillance studies, particularly those investigating serotypes in children under 5 years of age, to monitor vaccine effectiveness and pneumococcal population dynamic following implementation of PCV10 into routine immunisation.
Collapse
Affiliation(s)
- Alex J J Lister
- Faculty of Medicine and Institute for Life Sciences, Infectious Disease Epidemiology Group, University of Southampton, Mailpoint 814, Level C, Sir Henry Wellcome Laboratories, South Block, University Hospital Southampton Foundation NHS Trust, Southampton, SO16 6YD, UK
| | - Cheng Foh Le
- School of Biosciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Eddy Seong Guan Cheah
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman (UTAR), Kampar Campus, 31900, Kampar, Perak, Malaysia
| | - Mohd Nasir Mohd Desa
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - David W Cleary
- Faculty of Medicine and Institute for Life Sciences, Infectious Disease Epidemiology Group, University of Southampton, Mailpoint 814, Level C, Sir Henry Wellcome Laboratories, South Block, University Hospital Southampton Foundation NHS Trust, Southampton, SO16 6YD, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK
| | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, Infectious Disease Epidemiology Group, University of Southampton, Mailpoint 814, Level C, Sir Henry Wellcome Laboratories, South Block, University Hospital Southampton Foundation NHS Trust, Southampton, SO16 6YD, UK. .,NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK. .,Global Health Research Institute, University of Southampton, Southampton, UK. .,Institute for Research, Development and Innovation, International Medical University, Kuala Lumpur, Malaysia.
| |
Collapse
|