{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T12:52:18Z","timestamp":1786366338872,"version":"build-2736575974"},"reference-count":54,"publisher":"Microbiology Society","issue":"2","license":[{"start":{"date-parts":[[2022,2,23]],"date-time":"2022-02-23T00:00:00Z","timestamp":1645574400000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,23]]},"abstract":"The transmission dynamics of \n \n Streptococcus pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> in sub-Saharan Africa are poorly understood due to a lack of adequate epidemiological and genomic data. Here we leverage a longitudinal cohort from 21 neighbouring villages in rural Africa to study how closely related strains of \n \n S. pneumoniae<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> are shared among infants. We analysed 1074 pneumococcal genomes isolated from 102 infants from 21 villages. Strains were designated for unique serotype and sequence-type combinations, and we arbitrarily defined strain sharing where the pairwise genetic distance between strains could be accounted for by the mean within host intra-strain diversity. We used non-parametric statistical tests to assess the role of spatial distance and prolonged carriage on strain sharing using a logistic regression model. We recorded 458 carriage episodes including 318 (69.4\u200a%) where the carried strain was shared with at least one other infant. The odds of strain sharing varied significantly across villages (\u03c72<\/jats:sup>=47.5, df=21, P<\/jats:italic>-value <0.001). Infants in close proximity to each other were more likely to be involved in strain sharing, but we also show a considerable amount of strain sharing across longer distances. Close geographic proximity (<5\u2009km) between shared strains was associated with a significantly lower pairwise SNP distance compared to strains shared over longer distances (P<\/jats:italic>-value <0.005). Sustained carriage of a shared strain among the infants was significantly more likely to occur if they resided in villages within a 5\u2009km radius of each other (P<\/jats:italic>-value <0.005, OR 3.7). Conversely, where both infants were transiently colonized by the shared strain, they were more likely to reside in villages separated by over 15\u2009km (P<\/jats:italic>-value <0.05, OR 1.5). PCV7 serotypes were rare (13.5\u200a%) and were significantly less likely to be shared (P<\/jats:italic>-value <0.001, OR \u22121.07). Strain sharing was more likely to occur over short geographical distances, especially where accompanied by sustained colonization. Our results show that strain sharing is a useful proxy for studying transmission dynamics in an under-sampled population with limited genomic data. This article contains data hosted by Microreact.<\/jats:p>","DOI":"10.1099\/mgen.0.000732","type":"journal-article","created":{"date-parts":[[2022,2,4]],"date-time":"2022-02-04T14:17:26Z","timestamp":1643984246000},"source":"Crossref","is-referenced-by-count":4,"title":["Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints"],"prefix":"10.1099","volume":"8","author":[{"given":"Madikay","family":"Senghore","sequence":"first","affiliation":[{"name":"Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, 677 Huntington Ave, Boston, MA 02115, USA"},{"name":"WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The 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