Huebner RE, Dagan R, Porath N, Wasas AD, Klugman KP. Lack of utility of serotyping multiple colonies for detection of simultaneous nasopharyngeal carriage of different pneumococcal serotypes. Pediatr Infect Dis J. 2000;19(10):1017–20.
Article
CAS
PubMed
Google Scholar
Satzke C, Dunne EM, Porter BD, Klugman KP, Mulholland EK, PneuCarriage project g. The PneuCarriage Project: a multi-centre comparative study to identify the best serotyping methods for examining pneumococcal carriage in vaccine evaluation studies. PLoS Med. 2015;12(11):e1001903 discussion e1001903.
Article
PubMed
PubMed Central
Google Scholar
Manenzhe RI, Dube FS, Wright M, Lennard K, Mounaud S, Lo SW, et al. Characterization of pneumococcal colonization dynamics and antimicrobial resistance using shotgun metagenomic sequencing in intensively sampled South African infants. Front Public Health. 2020;8:543898.
Article
PubMed
PubMed Central
Google Scholar
Wright MS, McCorrison J, Gomez AM, Beck E, Harkins D, Shankar J, et al. Strain level Streptococcus colonization patterns during the first year of life. Front Microbiol. 2017;8:1661.
Article
PubMed
PubMed Central
Google Scholar
Bobay LM, Wissel EF, Raymann K. Strain structure and dynamics revealed by targeted deep sequencing of the honey bee gut microbiome. mSphere. 2020;5(4). https://doi.org/10.1128/mSphere.00694-20.
Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med. 2020;12(1):71.
Article
PubMed
PubMed Central
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Callahan BJ, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS, et al. High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Res. 2019;47(18):e103.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eren AM, Borisy GG, Huse SM, Mark Welch JL. Oligotyping analysis of the human oral microbiome. Proc Nat Acad Sci USA. 2014;111(28):E2875–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG, et al. Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol. 2013;4(12):1111-9.
Edgar RC, Flyvbjerg H. Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics. 2015;31(21):3476–82.
Article
CAS
PubMed
Google Scholar
Hathaway LJ, Brugger S, Martynova A, Aebi S, Muhlemann K. Use of the Agilent 2100 bioanalyzer for rapid and reproducible molecular typing of Streptococcus pneumoniae. J Clin Microbiol. 2007;45(3):803–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brugger SD, Hathaway LJ, Muhlemann K. Detection of Streptococcus pneumoniae strain cocolonization in the nasopharynx. J Clin Microbiol. 2009;47(6):1750–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brugger SD, Frey P, Aebi S, Hinds J, Muhlemann K. Multiple colonization with S. pneumoniae before and after introduction of the seven-valent conjugated pneumococcal polysaccharide vaccine. PLoS One. 2010;5(7):e11638.
Article
PubMed
PubMed Central
Google Scholar
Yang W, Kang X, Yang Q, Lin Y, Fang M. Review on the development of genotyping methods for assessing farm animal diversity. J Anim Sci Biotechnol. 2013;4(1):2.
Article
PubMed
PubMed Central
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490.
Article
PubMed
PubMed Central
Google Scholar
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W256–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mika M, Mack I, Korten I, Qi W, Aebi S, Frey U, et al. Dynamics of the nasal microbiota in infancy: a prospective cohort study. J Allergy Clin Immunol. 2015;135(4):905–912 e911.
Article
PubMed
Google Scholar
Fuchs O, Latzin P, Kuehni CE, Frey U. Cohort profile: the Bern infant lung development cohort. Int J Epidemiol. 2012;41(2):366–76.
Article
PubMed
Google Scholar
Mika M, Maurer J, Korten I, Allemann A, Aebi S, Brugger SD, et al. Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case-control study. Microbiome. 2017;5(1):85.
Article
PubMed
PubMed Central
Google Scholar
Carvalho Mda G, Tondella ML, McCaustland K, Weidlich L, McGee L, Mayer LW, et al. Evaluation and improvement of real-time PCR assays targeting lytA, ply, and psaA genes for detection of pneumococcal DNA. J Clin Microbiol. 2007;45(8):2460–6.
Article
PubMed
Google Scholar
Hilty M, Wuthrich D, Salter SJ, Engel H, Campbell S, Sa-Leao R, et al. Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages. Genome Biol Evol. 2014;6(12):3281–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pai R, Gertz RE, Beall B. Sequential multiplex PCR approach for determining capsular serotypes of Streptococcus pneumoniae isolates. J Clin Microbiol. 2006;44(1):124–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dube FS, Ramjith J, Gardner-Lubbe S, Nduru P, Robberts FJL, Wolter N, et al. Longitudinal characterization of nasopharyngeal colonization with Streptococcus pneumoniae in a South African birth cohort post 13-valent pneumococcal conjugate vaccine implementation. Sci Rep. 2018;8(1):12497.
Article
PubMed
PubMed Central
Google Scholar
Hill PC, Cheung YB, Akisanya A, Sankareh K, Lahai G, Greenwood BM, et al. Nasopharyngeal carriage of Streptococcus pneumoniae in Gambian infants: a longitudinal study. Clin Infect Dis. 2008;46(6):807–14.
Article
PubMed
Google Scholar
Murad C, Dunne EM, Sudigdoadi S, Fadlyana E, Tarigan R, Pell CL, et al. Pneumococcal carriage, density, and co-colonization dynamics: a longitudinal study in Indonesian infants. Int J Infect Dis. 2019;86:73–81.
Article
CAS
PubMed
Google Scholar
Abdeldaim GM, Stralin K, Olcen P, Blomberg J, Herrmann B. Toward a quantitative DNA-based definition of pneumococcal pneumonia: a comparison of Streptococcus pneumoniae target genes, with special reference to the Spn9802 fragment. Diagn Microbiol Infect Dis. 2008;60(2):143–50.
Article
CAS
PubMed
Google Scholar
Suzuki N, Yuyama M, Maeda S, Ogawa H, Mashiko K, Kiyoura Y. Genotypic identification of presumptive Streptococcus pneumoniae by PCR using four genes highly specific for S. pneumoniae. J Med Microbiol. 2006;55(Pt 6):709–14.
Article
CAS
PubMed
Google Scholar
Tavares DA, Handem S, Carvalho RJ, Paulo AC, de Lencastre H, Hinds J, et al. Identification of Streptococcus pneumoniae by a real-time PCR assay targeting SP2020. Sci Rep. 2019;9(1):3285.
Article
PubMed
PubMed Central
Google Scholar
Anyansi C, Straub TJ, Manson AL, Earl AM, Abeel T. Computational methods for strain-level microbial detection in colony and metagenome sequencing data. Front Microbiol. 2020;11:1925.
Article
PubMed
PubMed Central
Google Scholar
Tonkin-Hill G, Ling C, Chaguza C, Salter SJ, Hinfonthong P, Nikolaou E, et al. Pneumococcal within-host diversity during colonisation, transmission and treatment. bioRxiv. 2022:2022.2002.2020.480002.
Mauffrey F, Fournier E, Demczuk W, Martin I, Mulvey M, Martineau C, et al. Comparison of sequential multiplex PCR, sequetyping and whole genome sequencing for serotyping of Streptococcus pneumoniae. PLoS One. 2017;12(12):e0189163.
Article
PubMed
PubMed Central
Google Scholar
Heinsbroek E, Tafatatha T, Phiri A, Swarthout TD, Alaerts M, Crampin AC, et al. Pneumococcal carriage in households in Karonga District, Malawi, before and after introduction of 13-valent pneumococcal conjugate vaccination. Vaccine. 2018;36(48):7369–76.
Article
PubMed
PubMed Central
Google Scholar
Chaguza C, Senghore M, Bojang E, Lo SW, Ebruke C, Gladstone RA, et al. Carriage dynamics of pneumococcal serotypes in naturally colonized infants in a rural African setting during the first year of life. Front Pediatr. 2020;8:587730.
Article
PubMed
Google Scholar
Oyewole OR, Lang P, Albrich WC, Wissel K, Leib SL, Casanova C, et al. The impact of pneumococcal conjugate vaccine (PCV) coverage heterogeneities on the changing epidemiology of invasive pneumococcal disease in Switzerland, 2005-2019. Microorganisms. 2021;9(5). https://doi.org/10.3390/microorganisms9051078.
Althouse BM, Hammitt LL, Grant L, Wagner BG, Reid R, Larzelere-Hinton F, et al. Identifying transmission routes of Streptococcus pneumoniae and sources of acquisitions in high transmission communities. Epidemiol Infect. 2017;145(13):2750–8.
Article
CAS
PubMed
Google Scholar
Flasche S, Lipsitch M, Ojal J, Pinsent A. Estimating the contribution of different age strata to vaccine serotype pneumococcal transmission in the pre vaccine era: a modelling study. BMC Med. 2020;18(1):129.
Article
PubMed
PubMed Central
Google Scholar
Lipsitch M, Abdullahi O, D’Amour A, Xie W, Weinberger DM, Tchetgen Tchetgen E, et al. Estimating rates of carriage acquisition and clearance and competitive ability for pneumococcal serotypes in Kenya with a Markov transition model. Epidemiology. 2012;23(4):510–9.
Article
PubMed
PubMed Central
Google Scholar
Wyllie AL, Wijmenga-Monsuur AJ, van Houten MA, Bosch A, Groot JA, van Engelsdorp GJ, et al. Molecular surveillance of nasopharyngeal carriage of Streptococcus pneumoniae in children vaccinated with conjugated polysaccharide pneumococcal vaccines. Sci Rep. 2016;6:23809.
Article
CAS
PubMed
PubMed Central
Google Scholar
Valente C, Hinds J, Gould KA, Pinto FR, de Lencastre H, Sa-Leao R. Impact of the 13-valent pneumococcal conjugate vaccine on Streptococcus pneumoniae multiple serotype carriage. Vaccine. 2016;34(34):4072–8.
Article
CAS
PubMed
Google Scholar
Kandasamy R, Gurung M, Thapa A, Ndimah S, Adhikari N, Murdoch DR, et al. Multi-serotype pneumococcal nasopharyngeal carriage prevalence in vaccine naive Nepalese children, assessed using molecular serotyping. PLoS One. 2015;10(2):e0114286.
Article
PubMed
PubMed Central
Google Scholar
Chan KC, Subramanian R, Chong P, Nelson EA, Lam HS, Li AM, et al. Pneumococcal carriage in young children after introduction of PCV13 in Hong Kong. Vaccine. 2016;34(33):3867–74.
Article
PubMed
Google Scholar
Simell B, Auranen K, Kayhty H, Goldblatt D, Dagan R, O’Brien KL, et al. The fundamental link between pneumococcal carriage and disease. Expert Rev Vaccines. 2012;11(7):841–55.
Article
CAS
PubMed
Google Scholar
Allemann A, Frey PM, Brugger SD, Hilty M. Pneumococcal carriage and serotype variation before and after introduction of pneumococcal conjugate vaccines in patients with acute otitis media in Switzerland. Vaccine. 2017;35(15):1946–53.
Article
PubMed
Google Scholar