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Here, we examined the strain-level carriage and co-colonization dynamics of <jats:italic>Streptococcus pneumoniae<\/jats:italic>\u00a0in a Swiss birth cohort by PacBio single-molecule real-time (SMRT) sequencing of the <jats:italic>ply<\/jats:italic>NCR marker.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>A total of 872 nasal swab (NS) samples were included from 47 healthy infants during the first year of life. Pneumococcal carriage was determined based on the quantitative real-time polymerase chain reaction (qPCR) targeting the <jats:italic>lytA<\/jats:italic> gene. The <jats:italic>ply<\/jats:italic>NCR marker was amplified from 214 samples having <jats:italic>lytA<\/jats:italic>-based carriage for pneumococcal strain resolution. Amplicons were sequenced using SMRT technology, and sequences were analyzed with the DADA2 pipeline. In addition, pneumococcal serotypes were determined using conventional, multiplex PCR (cPCR).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>PCR-based <jats:italic>ply<\/jats:italic>NCR amplification demonstrated a 94.2% sensitivity and 100% specificity for <jats:italic>Streptococcus pneumoniae<\/jats:italic> if compared to <jats:italic>lytA<\/jats:italic> qPCR. The overall carriage prevalence was 63.8%, and pneumococcal co-colonization (\u2265 2 <jats:italic>ply<\/jats:italic>NCR amplicon sequence variants (ASVs)) was detected in 38\/213 (17.8%) sequenced samples with the relative proportion of the least abundant strain(s) ranging from 1.1 to 48.8% (median, 17.2%; IQR, 5.8\u201333.4%). The median age to first acquisition was 147 days, and having \u2265 2 siblings increased the risk of acquisition.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>The <jats:italic>ply<\/jats:italic>NCR amplicon sequencing is species-specific and enables pneumococcal strain resolution. We therefore recommend its application for longitudinal strain-level carriage studies of <jats:italic>Streptococcus pneumoniae<\/jats:italic>.<\/jats:p>\n                \n              <\/jats:sec>","DOI":"10.1186\/s40168-022-01344-6","type":"journal-article","created":{"date-parts":[[2022,9,22]],"date-time":"2022-09-22T13:15:36Z","timestamp":1663852536000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants"],"prefix":"10.1186","volume":"10","author":[{"given":"Oluwaseun Rume-Abiola","family":"Oyewole","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp","family":"Latzin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvio D.","family":"Brugger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Hilty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,9,22]]},"reference":[{"issue":"10","key":"1344_CR1","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1097\/00006454-200010000-00019","volume":"19","author":"RE Huebner","year":"2000","unstructured":"Huebner RE, Dagan R, Porath N, Wasas AD, Klugman KP. 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