Betts, Modupeh; (2022) Transcriptomic investigation of the adaptation of Streptococcus pneumoniae. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

Streptococcus pneumoniae colonises the human nasopharynx as a commensal but can translocate to the lungs, meninges, and blood to cause potentially fatal infections. These host niches exhibit diverse physiological environments. Differences in adaptation to these conditions may explain differences between serotypes and genotypes in their ability to colonise the human host, be transmitted, and to cause disease. RNA sequencing (RNA-Seq) was used to investigate adaptation of clinical S. pneumoniae strains to different stress environments. In Chapter 3, to establish the optimal experimental conditions, the effects of carbohydrate source, temperature, and iron concentrations on bacterial growth dynamics were evaluated. S. pneumoniae strains selected on the basis of their ability to be carried and cause disease, showed differential growth phenotypes. In Chapter 4, to facilitate robust transcriptomic analysis, high-quality genome assemblies of S. pneumoniae serotype 1 (highly invasive, rarely found in carriage) and serotype 6B (rarely invasive, highly carried) strains were generated and characterised. A pneumococcal transcriptomic analysis pipeline was developed in Chapter 5 by investigating the transcriptomic response of two single gene knockouts of S. pneumoniae serotype 6B lacking the biosynthesis genes fhs or proABC. These mutants have been shown to be attenuated in vivo and the aim was to identify the transcriptomic basis for this. Adaptation by fhs S. pneumoniae included upregulation of pathways involved in secondary metabolites biosynthesis and quorum sensing while the proABC S. pneumoniae was upregulated for carbohydrate metabolism pathways. In Chapters 6 and 7, the transcriptomic adaptations of S. pneumoniae serotype 1 and serotype 6B strains to altered iron and temperature levels were delineated respectively, indicating strain specific gene expression with the majority of differential regulation occurring in core pneumococcal genes. In Chapter 8, to pave the way for investigating the S. pneumoniae transcriptome in human samples, a challenge in pneumococcal research, an approach to directly isolate high-quality pneumococcal RNA from human carriers was developed. The work in this thesis provides new insights in the gene regulation of clinical S. pneumoniae strains under various environmental exposures.

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