Bioinformatic analysis of Streptococcus uberis genes and genomes

Streptococcus uberis is a Gram-positive, catalase-negative member of the family Streptococcaceae and is an important environmental pathogen primarily responsible for a significant amount of bovine intramammary infections. This thesis describes the sequencing and comparison of multiple strains from clinical and sub-clinical infections. Following de novo assembly, these are compared to the single reference strain (0140J). The assemblies of strains sequenced with two technologies (Illumina and SOLiD) were compared. From these assemblies, annotation allowed the comparison of gene content, the pan and core genomes and gene gain/loss of coding sequences associated with clustered regularly interspaced short palindromic repeats (CRISPRs), prophage and bacteriocin production. Identification of sequence variants allowed identification of highly conserved and highly variant genes. Inferred intraspecies and interspecies (host-S. uberis) protein-protein interaction networks revealed pathways of bovine proteins enriched with potentially interacting pathogen proteins. These identified known and predicted pathways and also novel interaction partners. This was the first “whole-genome” comparison of multiple S. uberis strains isolated from clinical vs non-clinical intramammary infections including the type virulent vs non-virulent strains. These data allowed the first insight into potential evolutionary forces behind virulence differences