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Micoli F, Romano MR, Carboni F, Adamo R, Berti F. Strengths and weaknesses of pneumococcal conjugate vaccines. Glycoconj J 2023; 40:135-148. [PMID: 36652051 PMCID: PMC10027807 DOI: 10.1007/s10719-023-10100-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 11/24/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023]
Abstract
Multivalent vaccines addressing an increasing number of Streptococcus pneumoniae types (7-, 10-, 13-, 15-, 20-valent) have been licensed over the last 22 years. The use of polysaccharide-protein conjugate vaccines has been pivotal in reducing the incidence of invasive pneumococcal disease despite the emergence of non-vaccine serotypes. Notwithstanding its undoubtable success, some weaknesses have called for continuous improvement of pneumococcal vaccination. For instance, despite their inclusion in pneumococcal conjugate vaccines, there are challenges associated with some serotypes. In particular, Streptococcus pneumoniae type 3 remains a major cause of invasive pneumococcal disease in several countries.Here a deep revision of the strengths and weaknesses of the licensed pneumococcal conjugate vaccines and other vaccine candidates currently in clinical development is reported.
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Chaguza C, Yang M, Jacques LC, Bentley SD, Kadioglu A. Serotype 1 pneumococcus: epidemiology, genomics, and disease mechanisms. Trends Microbiol 2022; 30:581-592. [PMID: 34949516 PMCID: PMC7613904 DOI: 10.1016/j.tim.2021.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022]
Abstract
Streptococcus pneumoniae (the 'pneumococcus') is a significant cause of morbidity and mortality worldwide, causing life-threatening diseases such as pneumonia, bacteraemia, and meningitis, with an annual death burden of over one million. Discovered over a century ago, pneumococcal serotype 1 (S1) is a significant cause of these life-threatening diseases. Our understanding of the epidemiology and biology of pneumococcal S1 has significantly improved over the past two decades, informing the development of preventative and surveillance strategies. However, many questions remain unanswered. Here, we review the current state of knowledge of pneumococcal S1, with a special emphasis on clinical epidemiology, genomics, and disease mechanisms.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Darwin College, University of Cambridge, Silver Street, Cambridge, UK; Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK; NIHR Mucosal Pathogens Research Unit, Division of Infection and Immunity, University College London, London, UK.
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK
| | - Laura C Jacques
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK.
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK; Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK
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Kellner JD, Ricketson LJ, Demczuk WHB, Martin I, Tyrrell GJ, Vanderkooi OG, Mulvey MR. Whole-Genome Analysis of Streptococcus pneumoniae Serotype 4 Causing Outbreak of Invasive Pneumococcal Disease, Alberta, Canada. Emerg Infect Dis 2021; 27:1867-1875. [PMID: 34152965 PMCID: PMC8237880 DOI: 10.3201/eid2707.204403] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
After the introduction of pneumococcal conjugate vaccines for children, invasive pneumococcal disease caused by Streptococcus pneumoniae serotype 4 declined in all ages in Alberta, Canada, but it has reemerged and spread in adults in Calgary, primarily among persons who are experiencing homelessness or who use illicit drugs. We conducted clinical and molecular analyses to examine the cases and isolates. Whole-genome sequencing analysis indicated relatively high genetic variability of serotype 4 isolates. Phylogenetic analysis identified 1 emergent sequence type (ST) 244 lineage primarily associated within Alberta and nationally distributed clades ST205 and ST695. Isolates from 6 subclades of the ST244 lineage clustered regionally, temporally, and by homeless status. In multivariable logistic regression, factors associated with serotype 4 invasive pneumococcal disease were being male, being <65 years of age, experiencing homelessness, having a diagnosis of pneumonia or empyema, or using illicit drugs.
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Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G, Winsor GL, Brinkman FSL. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2019; 45:W30-W35. [PMID: 28472413 PMCID: PMC5570257 DOI: 10.1093/nar/gkx343] [Citation(s) in RCA: 889] [Impact Index Per Article: 177.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/18/2017] [Indexed: 11/14/2022] Open
Abstract
IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer's integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.
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Affiliation(s)
- Claire Bertelli
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Matthew R Laird
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kelly P Williams
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA
| | | | - Britney Y Lau
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Gemma Hoad
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Baek JY, Kim SH, Kang CI, Chung DR, Peck KR, Ko KS, Song JH. Genome characterization of an extensively drug-resistant Streptococcus pneumoniae serotype 11A strain. Microbiol Immunol 2019; 63:206-212. [PMID: 31081554 DOI: 10.1111/1348-0421.12689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/18/2019] [Accepted: 05/01/2019] [Indexed: 11/27/2022]
Abstract
In this study, the whole genome sequences of two Streptococcus pneumoniae clinical isolates from South Korea were determined and compared. They were found to be the same serotype (11 A) and multilocus sequence typing analysis showed that they are single-locus variants (SLVs; ST8279 and ST166) of each other, differing at one allele (aroE). However, the ST8279 strain is extensively drug-resistant (XDR) whereas the ST166 strain is not. The genome of the XDR strain is very similar in structure to that of two previously reported genomes, AP200 (11 A:ST62) and 70585 (5:ST5803); however, some regions were inverted and there were some exogenous regions in the ST8279 strain. It was found that 6,502 single nucleotide polymorphisms are dispersed across the genome between the two serotype 11 A ST8279 and ST166 strains. Many of them are located in genes associated with antibiotic resistance. In addition, many amino acid differences were also identified in genes involved in DNA repair (mutL, uvrA and uvrC) and recombination (recU, recR and recA). On the basis of these results, it was inferred that the XDR strain did not evolve from its SLV via a single recombination event involving a large portion of the genome including the aroE gene. Rather, the strain likely evolved through many point mutations and recombination events involving small portions of the genome.
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Affiliation(s)
- Jin Yang Baek
- Asia Pacific Foundation for Infectious Diseases, Seoul, South Korea
| | - So Hyun Kim
- Asia Pacific Foundation for Infectious Diseases, Seoul, South Korea
| | - Cheol-In Kang
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Doo Ryeon Chung
- Asia Pacific Foundation for Infectious Diseases, Seoul, South Korea.,Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Kwan Soo Ko
- Asia Pacific Foundation for Infectious Diseases, Seoul, South Korea.,Department of Molecular Cell Biology and Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Jae-Hoon Song
- Asia Pacific Foundation for Infectious Diseases, Seoul, South Korea
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