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Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

Lees, JA; Croucher, NJ; Goldblatt, D; Nosten, F; Parkhill, J; Turner, C; Turner, P; (2017) Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration. eLIFE , 6 , Article e26255. 10.7554/eLife.26255. Green open access

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Abstract

Streptococcus pneumoniae is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, but variability in its duration is currently only understood at the serotype level. Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data, and combined these results with whole genome sequence data. We estimated that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas the host traits considered here (age and previous carriage) accounted for less than 5%. We further partitioned this heritability into both lineage and locus effects, and quantified the amount attributable to the largest sources of variation in carriage duration: serotype (17%), drug-resistance (9%) and other significant locus effects (7%). A pan-genome-wide association study identified prophage sequences as being associated with decreased carriage duration independent of serotype, potentially by disruption of the competence mechanism. These findings support theoretical models of pneumococcal competition and antibiotic resistance.

Type: Article
Title: Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.7554/eLife.26255
Language: English
Additional information: This article is published under Attribution 4.0 International (CC BY 4.0) License.
Keywords: evolutionary biology, genomics, infectious disease, microbiology
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health > Infection, Immunity and Inflammation Dept
URI: https://discovery.ucl.ac.uk/id/eprint/1567636
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