Senghore, Madikay, Chaguza, Chrispin 
ORCID: 0000-0002-2108-1757, Bojang, Ebrima, Tientcheu, Peggy-Estelle, Bancroft, Rowan E, Lo, Stephanie W, Gladstone, Rebecca A, McGee, Lesley, Worwui, Archibald, Foster-Nyarko, Ebenezer et al (show 9 more authors)
(2022)
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.
MICROBIAL GENOMICS, 8 (2).
000732-.
Abstract
The transmission dynamics of <i>Streptococcus pneumoniae</i> 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 <i>S. pneumoniae</i> 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 %) where the carried strain was shared with at least one other infant. The odds of strain sharing varied significantly across villages (χ<sup>2</sup>=47.5, df=21, <i>P</i>-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 km) between shared strains was associated with a significantly lower pairwise SNP distance compared to strains shared over longer distances (<i>P</i>-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 km radius of each other (<i>P</i>-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 km (<i>P</i>-value <0.05, OR 1.5). PCV7 serotypes were rare (13.5 %) and were significantly less likely to be shared (<i>P</i>-value <0.001, OR -1.07). 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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | pneumococcal transmission dynamics, rural African setting |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 19 May 2022 10:28 |
| Last Modified: | 14 Mar 2024 20:36 |
| DOI: | 10.1099/mgen.0.000732 |
| Open Access URL: | https://doi.org/10.1099/mgen.0.000732 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3155147 |
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