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O022 - CHARACTERISATION OF PNEUMOCOCCAL WITHIN-HOST DIVERSITY DURING TREATMENT, TRANSMISSION AND CARRIAGE VIA DEEP POPULATION SEQUENCING (ID 374)
Typically studies investigating the genomics of Streptococcus pneumoniae have used whole genome sequencing (WGS) of single colony isolates obtained by sequencing DNA after selecting an individual colony from a culture plate. Such studies provide limited insight into within-host genomic diversity, and can obscure cases of multiple carriage.
More than 3500 nasopharyngeal swab samples from the longitudinal Maela pneumococcal colonization study were plated onto selective Columbia nalidixic acid agar plates. All colonies were harvested from plates and DNA extracted for deep within-host population sequencing.
We demonstrate that population sequencing can accurately identify instances of multiple colonization and antimicrobial resistance elements. The increased resolution detected a greater prevalence of the invasive serotype 1 during carriage, and an elevated rate of transmission from mothers to their children in the first year of the child’s life. Accurate data on the administration of antimicrobials indicated that infants were at risk of both the acquisition and colonization of a multi drug resistant bacterium following antimicrobial treatment. Rates of co-colonisation imply that in the absence of treatment, susceptible lineages outcompete resistant lineages within the host.
The improved resolution and additional insights into co-colonisation, antimicrobial resistance, within-host selection and transmission indicate that deep within-host population sequencing can provide a general approach to enhance the genomic surveillance of S. pneumoniae and other pathogens.