Integrating traditional microbiology with cutting-edge (meta-)genomics to advance pathogen detection and to elucidate microbiome signatures of infection

Abstract

Microbes play a central role in human health. Through normal everyday activities, the human body is exposed to countless microorganisms from the environment in addition to the hundreds of species that colonize the human body and skin. A small fraction of them are pathogens, which can invade and damage the human body through direct or indirect means. How pathogens perform their in situ activities, interact with other host-associated microorganisms and what factors control such activities remains to be fully understood. The availability of high throughput omics technologies coupled with the development of fast, powerful computational tools for the assessment of the resulting big sequencing data have provided new opportunities to better examine pathogenic microbes, not only to accurately detect them and gain basic knowledge in their biology but also to understand how they evolve and interact with other pathogenic and non-pathogenic microorganisms in a multifaceted habitat as the human body. In this thesis, a series of studies are presented that integrated clinical microbiology, epidemiology and omics techniques to study bacterial pathogens, their diversity and evolution, and to elucidate how virulent bacteria disrupt the ecology of the healthy human microbiome, especially in the intestinal tract. In this regard, Chapter 2 presents a phylogenomic study performed to resolve the true relationships between C. botulinum and C. sporogenes, two closely related species that pose differential risk for human health, and assess the frequency of horizontal transfer of the diagnostic toxin gene. Chapter 3 presents a pathogenomic study of Bacillus anthracis plasmids pXO1 and pXO2, executed to detect, quantify and characterize the variation among these virulent plasmids. Chapter 4 presents a phylogenomic study executed to investigate the genome diversity, population structure, virulence potential, and antibiotic resistance profile of 279 pathogenic E. coli strains isolated from individuals with diarrhea and controls living in urban and rural regions in Northern Ecuador. Finally, Chapter 5 presents an epidemiology and metagenomic study focused on the detection of the causative agent of diarrhea and the characterization of the signature of Escherichia coli infection on the gut microbiome in same cohort of young children as in Chapter 4.