Winje BA, Vestrheim DF, White RA, Steens A. The risk of invasive pneumococcal disease differs between risk groups in Norway following widespread use of the 13-valent pneumococcal vaccine in children. Microorganisms. 2021;9. https://doi.org/10.3390/microorganisms9081774.

Løvlie A, Vestrheim DF, Aaberge IS, Steens A. Changes in pneumococcal carriage prevalence and factors associated with carriage in Norwegian children, four years after introduction of PCV13. BMC Infect Dis. 2020;20:29.

Article  PubMed  PubMed Central  Google Scholar 

Vaxneuvance pneumococcal polysaccharide conjugate vaccine, authorisation note. Available from: https://www.ema.europa.eu/en/medicines/human/EPAR/vaxneuvance. Cited 2024 Apr 17.

Prevenar 20 pneumococcal polysaccharide conjugate vaccine (20-valent, adsorbed), authorisation note. Available from: https://www.ema.europa.eu/en/medicines/human/EPAR/prevenar-20-previously-apexxnar. Cited 2024 Apr 17.

Kapatai G, Sheppard CL, Al-Shahib A, Litt DJ, Underwood AP, Harrison TG, et al. Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline. PeerJ. 2016;4: e2477.

Article  PubMed  PubMed Central  Google Scholar 

Bentley SD, Aanensen DM, Mavroidi A, Saunders D, Rabbinowitsch E, Collins M, et al. Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. PLoS Genet. 2006;2. Available from: https://pubmed.ncbi.nlm.nih.gov/16532061/. Cited 2024 Mar 3.

Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, et al. Selective and genetic constraints on pneumococcal serotype switching. PLoS Genet. 2015;11: e1005095.

Article  PubMed  PubMed Central  Google Scholar 

Bradshaw JL, Rafiqullah IM, Robinson DA, McDaniel LS. Transformation of nonencapsulated Streptococcus pneumoniae during systemic infection. Sci Rep. 2020;10:18932.

Article  PubMed  PubMed Central  Google Scholar 

Croucher NJ, Hanage WP, Harris SR, McGee L, van der Linden M, de Lencastre H, et al. Variable recombination dynamics during the emergence, transmission and “disarming” of a multidrug-resistant pneumococcal clone. BMC Biol. 2014;12:49.

Article  PubMed  PubMed Central  Google Scholar 

Weinberger DM, Malley R, Lipsitch M. Serotype replacement in disease after pneumococcal vaccination. Lancet. 2011;378:1962–73.

Article  PubMed  PubMed Central  Google Scholar 

Lo SW, Gladstone RA, van Tonder AJ, Lees JA, du Plessis M, Benisty R, et al. Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study. Lancet Infect Dis. 2019;19:759–69.

Article  PubMed  PubMed Central  Google Scholar 

Luck JN, Tettelin H, Orihuela CJ. Sugar-coated killer: serotype 3 pneumococcal disease. Front Cell Infect Microbiol. 2020;10: 613287.

Article  PubMed  PubMed Central  Google Scholar 

Park IH, Pritchard DG, Cartee R, Brandao A, Brandileone MCC, Nahm MH. Discovery of a new capsular serotype (6C) within serogroup 6 of Streptococcus pneumoniae. J Clin Microbiol. 2007;45:1225–33.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Feemster K, Weaver J, Buchwald U, Banniettis N, Cox KS, McIntosh ED, et al. Pneumococcal vaccine breakthrough and failure in infants and children: a narrative review. Vaccines (Basel). 2023;11. https://doi.org/10.3390/vaccines11121750.

Corander J, Fraser C, Gutmann MU, Arnold B, Hanage WP, Bentley SD, et al. Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. Nat Ecol Evol. 2017;1:1950–60.

Article  PubMed  PubMed Central  Google Scholar 

Gladstone RA, Devine V, Jones J, Cleary D, Jefferies JM, Bentley SD, et al. Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK. Microb Genom. 2017;3: e000119.

PubMed  PubMed Central  Google Scholar 

Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ, Corander J, et al. International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine. 2019;43:338–46.

Article  PubMed  PubMed Central  Google Scholar 

Li Y, Metcalf BJ, Chochua S, Li Z, Gertz RE Jr, Walker H, et al. Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences. BMC Genomics. 2017;18:621.

Article  PubMed  PubMed Central  Google Scholar 

Epping L, van Tonder AJ, Gladstone RA, The Global Pneumococcal Sequencing Consortium, Bentley SD, Page AJ, et al. SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data. Microb Genom. 2018;4. https://doi.org/10.1099/mgen.0.000186.

The Global Pneumococcal Sequencing Project. Available from: https://www.pneumogen.net/gps/.

Pathogenwatch. A global platform for genomic surveillance. Available from: https://www.pathogen.watch.

Monocle data viewer. Available from: https://data-viewer.monocle.sanger.ac.uk/project/gps.

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, et al. Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Res. 2019;29:304–16.

Article  CAS  PubMed  PubMed Central  Google Scholar 

GPS tools. Available from: https://www.pneumogen.net.

Wickham H, François R, Henry L, Müller K, Vaughan D. dplyr: a grammar of data manipulation. 2023. Available from: https://dplyr.tidyverse.org.

Wickham H. ggplot2: Elegant Graphics for Data Analysis. New York: Springer-Verlag; 2016. See: https://ggplot2.tidyverse.org/authors.html#citation.

Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, et al. Welcome to the tidyverse . J Open Source Softw. 2019:1686. https://doi.org/10.21105/joss.01686.

Neuwirth E. RColorBrewer: ColorBrewer Palettes. R package version 1.1-3. 2022. Available from: https://doi.org/10.32614/cran.package.rcolorbrewer.

Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021;7. https://doi.org/10.1099/mgen.0.000685.

Seeman T. Snippy. Available from: https://github.com/tseemann/snippy.

Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 2015;43: e15.

Article  PubMed  Google Scholar 

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37:1530–4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Didelot X, Croucher NJ, Bentley SD, Harris SR, Wilson DJ. Bayesian inference of ancestral dates on bacterial phylogenetic trees. Nucleic Acids Res. 2018;46: e134.

Article  PubMed  PubMed Central  Google Scholar 

Drummond AJ, Suchard MA, Xie Dong, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29:1969–73. https://doi.org/10.1093/molbev/mss075.

Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM, Harris SR. Phandango: an interactive viewer for bacterial population genomics. Bioinformatics. 2018;34:292–3.

Article  CAS  PubMed  Google Scholar 

The Norwegian Surveillance System for Communicable Diseases. MSIS-statistikk. Available from: https://www.msis.no/.

Vestrheim DF, Høiby EA, Aaberge IS, Caugant DA. Impact of a pneumococcal conjugate vaccination program on carriage among children in Norway. Clin Vaccine Immunol. 2010;17:325–34.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Savulescu C, Krizova P, Valentiner-Branth P, Ladhani S, Rinta-Kokko H, Levy C, et al. Effectiveness of 10 and 13-valent pneumococcal conjugate vaccines against invasive pneumococcal disease in European children: SpIDnet observational multicentre study. Vaccine. 2022;40:3963–74.

Article  CAS  PubMed  Google Scholar 

Groves N, Sheppard CL, Litt D, Rose S, Silva A, Njoku N, et al. Evolution of Streptococcus pneumoniae serotype 3 in England and Wales: a major vaccine evader. Genes. 2019;10. https://doi.org/10.3390/genes10110845.

Palmborg A, Skovdal M, Molden T, Åhman H, Chen L, Banefelt J. Invasive pneumococcal disease among the elderly in the later era of paediatric pneumococcal conjugate vaccination-a longitudinal study over 10 years based on public surveillance data in the Nordics. PLoS ONE. 2023;18: e0287378.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Swarthout TD, Henrion MYR, Thindwa D, Meiring JE, Mbewe M, Kalizang’Oma A, et al. Waning of antibody levels induced by a 13-valent pneumococcal conjugate vaccine, using a 3 + 0 schedule, within the first year of life among children younger than 5 years in Blantyre, Malawi: an observational, population-level, serosurveillance study. Lancet Infect Dis. 2022;22:1737–47.

Article  CAS  PubMed  PubMed Central