{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T02:11:32Z","timestamp":1790734292460,"version":"4.1.0"},"reference-count":54,"publisher":"Microbiology Society","issue":"3","license":[{"start":{"date-parts":[[2022,3,1]],"date-time":"2022-03-01T00:00:00Z","timestamp":1646092800000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000053","name":"National Eye Institute","doi-asserted-by":"crossref","award":["EY031600"],"award-info":[{"award-number":["EY031600"]}],"id":[{"id":"10.13039\/100000053","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000053","name":"National Eye Institute","doi-asserted-by":"crossref","award":["EY024285"],"award-info":[{"award-number":["EY024285"]}],"id":[{"id":"10.13039\/100000053","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100007745","name":"Massachusetts Lions Eye Research Fund","doi-asserted-by":"crossref","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/100007745","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,1]]},"abstract":"\n \n \n Streptococcus pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> is a leading cause of ocular infections including serious and sight-threatening conditions. The use of pneumococcal conjugate vaccines (PCV) has substantially reduced the incidence of pneumonia and invasive pneumococcal diseases, but has had limited impact on ocular infections. Additionally, widespread vaccine use has resulted in ongoing selective pressure and serotype replacement in carriage and disease. To gain insight into the population structure of pneumococcal isolates causing ocular infections in a post-PCV-13 time period, we investigated the genomic epidemiology of ocular \n \n S. pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> isolates (n<\/jats:italic>=45) collected at Massachusetts Eye and Ear between 2014 and 2017. By performing a series of molecular typing methods from draft genomes, we found that the population structure of ocular \n \n S. pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> is highly diverse with 27 sequence types (grouped into 18 clonal complexes) and 17 serotypes being identified. Distribution of these lineages diverged according to the site of isolation, with conjunctivitis being commonly caused by isolates grouped in the Epidemic Conjunctivitis Cluster-ECC (60\u200a%), and ST448 (53.3\u200a%) being most frequently identified. Conversely, \n \n S. pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> keratitis cases were caused by a highly diverse population of isolates grouping within 15 different clonal complexes. Serotyping inference demonstrated that 95.5\u200a% of the isolates were non-PCV-13 vaccine types. Most of the conjunctivitis isolates (80\u200a%) were unencapsulated, with the remaining belonging to serotypes 15B, 3 and 23B. On the other hand, \n \n S. pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> causing keratitis were predominantly encapsulated (95.2\u200a%) with 13 different serotypes identified, mostly being non-vaccine types. Carriage of macrolide resistance genes was common in our ocular \n \n S. pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> population (42.2\u200a%), and usually associated with the mefA +msrD<\/jats:italic> genotype (n<\/jats:italic>=15). These genes were located in the Macrolide Efflux Genetic Assembly cassette and were associated with low-level in vitro<\/jats:italic> resistance to 14- and 15-membered macrolides. Less frequently, macrolide-resistant isolates carried an ermB<\/jats:italic> gene (n<\/jats:italic>=4), which was co-located with the tet<\/jats:italic>M gene in a Tn-916-like transposon. Our study demonstrates that the population structure of ocular \n \n S. pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> is highly diverse, mainly composed by isolates that escape the PCV-13 vaccine, with patterns of tissue\/niche segregation, adaptation and specialization. These findings suggest that the population structure of ocular pneumococcus may be shaped by multiple factors including PCV-13 selective pressure, microbial-related and niche-specific host-associated features.<\/jats:p>","DOI":"10.1099\/mgen.0.000763","type":"journal-article","created":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T14:16:13Z","timestamp":1646662573000},"source":"Crossref","is-referenced-by-count":6,"title":["Population structure of ocular Streptococcus pneumoniae is highly diverse and formed by lineages that escape current vaccines"],"prefix":"10.1099","volume":"8","author":[{"given":"Camille","family":"Andre","sequence":"first","affiliation":[{"name":"Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA"},{"name":"Infectious Disease Institute, Boston, MA 02114, 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