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In this thesis, I bring into conversation two political theoretical frameworks -- decolonial thought and new materialism – with the South Korean novella The Vegetarian. I suggest that the novella, especially through its protagonist, performs a form of agency which calls for a reading that hinges not on the pursuit of definitive analysis but on the recognition of a personal, affective interaction with violent status quo sensibilities. I demonstrate that there exist understandings of agency within decolonial thought and new materialism which could be attuned to this call. I suggest a method that relies upon two thinkers in these frameworks for reading the novella, and after reading the novella through this method and transparently reflecting on my own role in these texts' encounter, I demonstrate that this way of simultaneously reading the novella and the theoretical texts has the capacity to affirm the open and uncertain mutual changes that happen at their encounter. Master of Arts In this thesis, I bring into conversation two political theoretical schools of thought -- decolonial thought and new materialism – with the South Korean novella The Vegetarian. I suggest that the novella demonstrates a unique agency which calls for a reading that is centered not on the pursuit of definitive analysis but on the recognition of a personal, affective interaction with status quo violence. I demonstrate that there exist understandings of agency within decolonial thought and new materialism which could be attuned to this call. I suggest a method that relies upon two thinkers in these frameworks for reading the novella, and after reading the novella through this method and transparently reflecting on my own role in these texts’ encounter, I demonstrate that this way of simultaneously reading the novella and the theoretical texts has the capacity to affirm the open and uncertain mutual changes that happen at their encounter.

The bacterium Burkholderia pseudomallei causes melioidosis, a rare but serious illness that can be fatal if untreated or misdiagnosed. Species-specific PCR assays provide a technically simple method for differentiating B. pseudomallei from near-neighbor species. However, substantial genetic diversity and high levels of recombination within this species reduce the likelihood that molecular signatures will differentiate all B. pseudomallei from other Burkholderiaceae. Currently available molecular assays for B. pseudomallei detection lack rigorous validation across large in silico datasets and isolate collections to test for specificity, and none have been subjected to stringent quality control criteria (accuracy, precision, selectivity, limit of quantitation (LoQ), limit of detection (LoD), linearity, ruggedness and robustness) to determine their suitability for environmental, clinical or forensic investigations. In this study, we developed two novel B. pseudomallei specific assays, 122018 and 266152, using a dual-probe approach to differentiate B. pseudomallei from B. thailandensis, B. oklahomensis and B. thailandensis-like species; other species failed to amplify. Species specificity was validated across a large DNA panel (>2,300 samples) comprising Burkholderia spp. and non-Burkholderia bacterial and fungal species of clinical and environmental relevance. Comparison of assay specificity to two previously published B. pseudomallei-specific assays, BurkDiff and TTS1, demonstrated comparable performance of all assays, providing between 99.7 and 100% specificity against our isolate panel. Last, we subjected 122018 and 266152 to rigorous quality control analyses, thus providing quantitative limits of assay performance. Using B. pseudomallei as a model, our study provides a framework for comprehensive quantitative validation of molecular assays and provides additional, highly validated B. pseudomallei assays for the scientific research community.

Little is currently known about bacterial pathogen evolution and adaptation within the host during acute infection. Previous studies of Burkholderia pseudomallei, the etiologic agent of melioidosis, have shown that this opportunistic pathogen mutates rapidly both in vitro and in vivo at tandemly repeated loci, making this organism a relevant model for studying short-term evolution. In the current study, B. pseudomallei isolates cultured from multiple body sites from four Thai patients with disseminated melioidosis were subjected to fine-scale genotyping using multilocus variable-number tandem repeat analysis (MLVA). In order to understand and model the in vivo variable-number tandem repeat (VNTR) mutational process, we characterized the patterns and rates of mutations in vitro through parallel serial passage experiments of B. pseudomallei. Despite the short period of infection, substantial divergence from the putative founder genotype was observed in all four melioidosis cases. This study presents a paradigm for examining bacterial evolution over the short timescale of an acute infection. Further studies are required to determine whether the mutational process leads to phenotypic alterations that impact upon bacterial fitness in vivo. Our findings have important implications for future sampling strategies, since colonies in a single clinical sample may be genetically heterogeneous, and organisms in a culture taken late in the infective process may have undergone considerable genetic change compared with the founder inoculum., Author Summary While both viral and bacterial pathogens have been shown to undergo genetic changes over the course of a chronic infection, this phenomenon has not been studied during an acute infection and as such is not well understood. Here, we examined within-host evolution of the pathogen Burkholderia pseudomallei during acute infection. B. pseudomallei causes the disease melioidosis, a significant cause of morbidity and mortality in many tropical regions of the world. We obtained multiple B. pseudomallei colonies from several tissue sites of four patients presenting with acute melioidosis in order to characterize how this bacterium evolves within the human host over a short period of time. By monitoring changes in rapidly evolving genetic regions, we found high levels of diversity of B. pseudomallei populations within a single patient, and even within a single body site. Comparison of these within-host mutation rates with in vitro mutation data enabled us to identify the most likely spatial migration of within-host populations and correlate these findings with clinical data to determine, in most cases, the origin of infection. Our study provides new insights into the evolution of bacterial pathogens during an acute infection, and lays the foundation for similar studies in other infectious agents.

Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST). These populations correlate with the major foci of endemicity (Australia and Southeast Asia). Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs). Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic characteristics and provides a rapid reference for epidemiologists wishing to track the origin of infection without the need to compile population data and learn population assignment algorithms., Author Summary Burkholderia pseudomallei is a soil-dwelling bacterium that can infect a large range of hosts. In humans, B. pseudomallei causes melioidosis, and typical routes of entry include open wounds, inhalation, or ingestion. Clinical features are diverse, although pneumonia and abscess formation are common. High rates of recombination within the genome of this bacterium have confounded attempts to match clinical samples to geographically defined populations. Here we provide a reference that simplifies source attribution issues. We applied population assignment software to previously generated sequence data from seven B. pseudomallei genes to define the major geographic populations within this species. We evaluated the robustness of our results by comparison with two additional population assignment programs. We present the likelihood that each variant is assigned to a particular geographic population. This information can be used to assign novel B. pseudomallei isolates to a geographic population without needing to learn and run cumbersome population assignment applications. This method can also be used for other bacteria that are difficult to source-attribute due to high levels of genomic variation and recombination.

Melioidosis is caused by Burkholderia pseudomallei, a Gram-negative bacillus, primarily found in soils in Southeast Asia and northern Australia. A recent case of melioidosis in non-endemic Arizona was determined to be the result of locally acquired infection, as the patient had no travel history to endemic regions and no previous history of disease. Diagnosis of the case was confirmed through multiple microbiologic and molecular techniques. To enhance the epidemiological analysis, we conducted several molecular genotyping procedures, including multi-locus sequence typing, SNP-profiling, and whole genome sequence typing. Each technique has different molecular epidemiologic advantages, all of which provided evidence that the infecting strain was most similar to those found in Southeast Asia, possibly originating in, or around, Malaysia. Advancements in new typing technologies provide genotyping resolution not previously available to public health investigators, allowing for more accurate source identification., Author Summary Melioidosis is a bacterial disease caused by percutaneous inoculation, aspiration or ingestion of the soil bacteria Burkholderia pseudomallei. Melioidosis is primarily found in Southeast Asia and Northern Australia, and, to a lesser degree, nearby regions. A recent case of melioidosis in Southwestern United States (Southern Arizona) prompted a detailed epidemiological and molecular investigation to discover the source of infection. The authors describe the use of multiple genomic analysis tools to aid in this investigation. The results of these analyses uniformly identified Southeast Asia as the source of the strain that infected the patient, however the epidemiological investigation had determined the patient had no international travel or known exposures to Southeast Asian products. New cutting edge technologies, such as next generation sequencing, are quickly being adapted into epidemiologic investigations, particularly for cases and outbreaks of unknown origin, although older, mature technologies with larger existing databases will still be needed for appropriate comparative analyses.

BackgroundThe island of New Guinea is located midway between the world's two major melioidosis endemic regions of Australia and Southeast Asia. Previous studies in Papua New Guinea have demonstrated autochthonous melioidosis in Balimo, Western province. In contrast to other regions of endemicity, isolates recovered from both environmental and clinical sources demonstrate narrow genetic diversity over large spatial and temporal scales.Methodology/principal findingsWe employed molecular typing techniques to determine the phylogenetic relationships of these isolates to each other and to others worldwide to aid in understanding the origins of the Papua New Guinean isolates. Multi-locus sequence typing of the 39 isolates resolved three unique sequence types. Phylogenetic reconstruction and Structure analysis determined that all isolates were genetically closer to those from Australia than those from Southeast Asia. Gene cluster analysis however, identified a Yersinia-like fimbrial gene cluster predominantly found among Burkholderia pseudomallei derived from Southeast Asia. Higher resolution VNTR typing and phylogenetic reconstruction of the Balimo isolates resolved 24 genotypes with long branch lengths. These findings are congruent with long term persistence in the region and a high level of environmental stability.Conclusions/significanceGiven that anthropogenic influence has been hypothesized as a mechanism for the dispersal of B. pseudomallei, these findings correlate with limited movement of the indigenous people in the region. The palaeogeographical and anthropogenic history of Australasia and the results from this study indicate that New Guinea is an important region for the further study of B. pseudomallei origins and dissemination.