Exploring the Evolution of Pathogenicity in a Mult-host Bacterial Pathogen Using Comparative Genomics

Abstract

Pantoea is a Gram-negative bacterial genus within the recently created Erwiniaceae. Pantoea members are found in association with a wide range of hosts, and some species have been reported as the causative agent of human infections. Despite this, little research has focused on the human pathogenicity of Pantoea. This thesis aims to explore the evolution of pathogenicity in Pantoea using phylogenetic and comparative genomic approaches, with a focus on human pathogenicity. Chapter 1 provides a broad review of Pantoea, virulence, and phylogenetic and genomic concepts. Chapter 2 describes molecular typing of clinical Pantoea isolates obtained from hospital patients. Of 54 clinical isolates, 41 were confirmed as Pantoea, with the majority of these isolates found to belong to P. septica. Chapter 3 involves verification of the taxonomy of Pantoea, the P. septica lineage, and the Erwiniaceae using phylogenomics. From over 100 strains, a 308 core protein dataset was used to perform a phylogenetic analysis. Genomes of all strains were used to conduct average nucleotide identity and average amino acid identity analyses. The phylogenetic analysis showed that the P. septica lineage, including the proposed genus Kalamiella, nested within Pantoea with strong support. This work indicates no basis for establishment of Kalamiella, or taxonomic revision of the P. septica lineage. Chapter 4 involves characterizing the evolutionary history of siderophore gene clusters in Pantoea. Siderophores are noted virulence factors involved in iron acquisition; however, the siderophore complement of Pantoea has been largely unexplored. Through comparative genomic and phylogenetic analyses, biosynthetic gene clusters for three distinct siderophores were found across Pantoea, with each having a unique distribution and evolutionary history. Notably, the aerobactin gene cluster was acquired by two human pathogenic species, P. septica and P. ananatis, in two independent horizontal transfer events; both from human pathogenic genera of Enterobacteriaceae. This thesis confirmed the identity of dozens of human Pantoea isolates and demonstrated that P. septica specifically appears to be adept at infecting humans. This work also validated the taxonomic assignment of the P. septica lineage as part of Pantoea and provided evidence of virulence factor horizontal acquisition by P. septica from established human pathogens.