Understanding phage-host interactions in Staphylococcus aureus through population genomics and bioinformatics Open Access
Moller, Abraham (Spring 2021)
Abstract
This dissertation seeks to understand the host basis of phage host range in Staphylococcus aureus with the ultimate goal of improving phage therapy against S. aureus infections. Increasing antibiotic resistance, high prevalence, and failure to develop vaccines makes alternative S. aureus therapies such as phage therapy crucial. However, while S. aureus phages have long been known to have broad host ranges, the mechanism behind the resistant exceptions remains unknown. This paradox justified comprehensive, population-wide studies to understand determinants of phage host range in S. aureus on a species rather than strain-wide level. In my dissertation, I not only reviewed the literature to identify what is known about host range and resistance factors in the species but also used population genomics to discover new host range factors and examine the evolution of known factors in the species. I found that host resistance factors have been identified and characterized at three stages of the infection cycle (adsorption, biosynthesis, and assembly) but neither uptake nor lysis stages. I also hypothesized that these factors determine host range in a phylogenetically hierarchical manner given their respective conservation in the species. GWAS identified novel core genes involved in host range and known host range determinants but significant determinants only partially explained the phenotype in predictive modeling. Molecular genetic techniques (backcrossing and complementation) confirmed a subset of novel determinants did have causal associations with the phenotype. Regarding phage resistance evolution, I found adsorption genes to be the most conserved in the database, core phage resistance genes functional, diverse, and under purifying selection like core genes overall. Only superinfection immunity correlated with temperate phage resistance or accessory genome content, but overall phage resistance gene presence never correlated with virulent phage resistance. All genes exhibited some level of phylogenetic signal, but it was weakest amongst the assembly genes. I also developed a sequence-based assay with the future potential to rapidly determine phage susceptibility of clinical isolates. I found that the limit of detection was close to minor allele frequency average (~5-7%), I could detect VISA-causing mutations in clinical strains, and I could discriminate clinical VSSA from VISA strains.
Table of Contents
Chapter 1: Introduction……………………………………………………………………………………...1
Chapter 2: Determinants of Phage Host Range in Staphylococcus Species…………………………………34
Chapter 3: Genes influencing phage host range in Staphylococcus aureus on a species-wide scale………….58
Supplemental Material for Chapter 3……………………………………………………………………....103
Chapter 4: Species-scale genomic analysis of known phage resistance mechanisms and their relationships to horizontal gene transfer in S. aureus……………………………………………………………………….148
Chapter 5: Development of an amplicon nanopore sequencing strategy for detection of mutations conferring intermediate resistance to vancomycin in Staphylococcus aureus strains…………………………………...200
Chapter 6: Conclusions……………………………………………………………………………………219
Chapter 7: Bibliography…………………………………………………………………………………....229
About this Dissertation
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Understanding phage-host interactions in Staphylococcus aureus through population genomics and bioinformatics () | 2021-05-10 08:54:44 -0400 |
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Supplemental Files
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