Date of Award
Doctor of Philosophy (PhD)
Bacterial pathogens have been a historical scourge for the entirety of human existence but have been significantly thwarted since the 20th century due to the development of antibiotics. However, owing to the large selection pressure of antibiotics on bacterial populations, phenotypic antibiotic resistance from the development of vertically transmitted mutations and horizontally acquired antibiotic resistance genes (ARGs) is increasing. The sum has produced multidrug resistant organisms (MDROs) which have extremely limited treatment options. Epidemiological studies have determined that carbapenem resistant Enterobacteriaceae (CRE), Acinetobacter baumannii, and vancomycin resistant Enterococcus (VRE) are some of the most problematic MDRO infections. The advent of cost-effective and accurate next-generation sequencing has resulted in a proliferation of bacterial genomes available. ARGs, antibiotic resistance conferring single nucleotide polymorphism (SNPs), and virulence genes can be identified within an assembled genome by comparison to known databases. The combination of the genetic information encoded within the genome of an isolate along with metadata related to important phenotypes or clinical context can be used to identify trends in ARG carriage, evolution over time, and viii differences in gene burden. This information can also be used in understanding the effects of antibiotic treatment on multi organism infections such as bacterial vaginosis. My thesis intends to investigate features related to natural populations of bacterial isolates in the Enterobacteriaceae family and Acinetobacter baumannii in Chapters 2, 3, 4 and the Gram-positive organisms Enterococcus faecium, Gardnerella, and Corynebacterium in Chapters 5, 6, and 7. In Chapter 2 we identify the carbapenem resistance gene blaIMP-27 in a clinical isolate of carbapenem resistance Providencia rettgeri. We then acquired two blaIMP-27 bearing Proteus mirabilis and determine that one isolate (PM187) also has it on a plasmid. We were able to completely close the blaIMP-27 bearing plasmids pPR1 and pPM187 and determine that the local genetic context was similar but the background of the plasmids were different. In Chapter 3 we collect a cohort of longitudinally antibiotic resistant organisms recovered from hospital surfaces in the United States and Pakistan. We compare the phenotypic identification with the genomic identification to determine that several isolates represent novel taxonomic groups, we identify a severe degree of phenotypic antibiotic resistance in the collected important human pathogens and elucidate a network of ARGs common amongst the bacteria. Importantly, we demonstrate that E. faecium and A. baumannii co-occur greater than predicted by chance a lone and that laboratory strains of these organisms are capable of forming synergistic growth in biofilms. In Chapter 4 we collect a cohort of Klebsiella variicola from Washington University and use whole genome sequencing to determine the population structure of all publicly available K. variicola genomes and identify genes relevant for infection related phenotypes. We show that these differences may have a functional consequence as some K. variicola strains can be more competent uropathogens than Klebsiella pneumoniae. In Chapter 5 we compare linezolid resistance mechanisms within a cohort to VRE from the United States and Pakistan to determine that all of the US isolates were resistant due to SNPs in the 23S rRNA sequence, but the Pakistan isolates all had acquired ARGs. Two of six these ARGs were the limited scope efflux pumps optrA and poxtA but the other ARGs are novel variants of the cfr family. In Chapter 6 we analyze a set of publicly available Gardnerella vaginalis genomes and metatranscriptomes of women with bacterial vaginosis to determine that what is commonly considered a single species can be interpreted as 9 different species with differences in accessory genome function and varying presence in bacterial vaginosis cases. Different genomospecies are present at varying abundance and putative virulence genes have high expression values during infection. Finally, in chapter 7 we determine the effects of acquired daptomycin resistance on the biology of Corynebacterium striatum. In summation this work provides novel insights on the relatedness of important human pathogens to one another and the content of their genes relevant toward infection across a wide range of species.
Chair and Committee
Megan Baldridge, Carey-Ann Burnham, Mario Feldman, Jim Fleckenstein, Stephanie Fritz, Andy Kau
Potter, Robert, "Genomic analysis of diverse bacterial pathogens" (2020). Arts & Sciences Electronic Theses and Dissertations. 2336.