Dissertation

Long Term Local Persistence of Yersinia pestis in Arizona

Ballard, Rebecca G

2024

Overview

Plague is a rapidly progressing and often fatal zoonotic disease caused by the bacterium Yersinia pestis. This pathogen has impacted humans for millennia, especially during three major pandemics that resulted in over 200 million deaths. During the third pandemic, plague was involved in a global spreading event, and it is now ecologically established on five continents, including North America. Although plague has historically had major implications for humans, in North America it is now primarily a disease of rodents and their associated fleas. Plague cycles between amplifying events where disease transmission is rapid (epizootics), and low-level persistence cycles (enzootics). It is during epizootic events that large die offs of infected rodent species are documented, and infected fleas can feed on humans. This results in the most common clinical presentation of the disease in humans, bubonic plague. Bubonic plague is acquired via flea vectors and, if left untreated, has a 40-60% mortality rate. Bubonic plague can progress to the less common but more fatal form of the disease, pneumonic plague, which approaches 100% mortality within 1-5 days of disease onset (8). Although outbreaks of sylvatic plague in the southwestern US are well documented, the mechanisms by which Y. pestis persists are unknown. Sylvatic plague is defined as a flea-borne disease in wild rodents. Sampling efforts to detect this disease during inter-epizootic periods yield low or no detection of Y. pestis. Previous studies examining multi-locus variable number tandem repeat loci (MLVA) in Y. pestis have shown local differentiation when examined at one time point (7), but data needed to sufficiently analyze persistence through time for this pathogen is not readily available. This study examines Y. pestis genomic diversity across time (2001-2020) and space (nine locations) near Flagstaff, Arizona, USA and utilizes archived flea DNA extracts that were collected for public health purposes. Therefore, due to a limited number of fleas collected at each site, not all sites had additional fleas that could be used for culturing of Y. pestis. Complex DNA extracts obtained from whole fleas are poor candidates for whole genome sequencing of Y. pestis due to low burden of pathogen and therefore would produce low coverage of the Y. pestis genome. Therefore, to characterize Y. pestis genomes present in these flea samples, culture methods to obtain pure isolates and targeted Y. pestis DNA capture and enrichment were used and whole genome sequenced. Target enrichment uses of RNA probes to capture the genome of Y. pestis present in the flea DNA extractions. Genomic data from both enrichment and cultured samples revealed two main phylogenetic lineages of Y. pestis located in east and west Flagstaff, each with multiple subclades. In most cases, samples within a (the same?) subclade were found within ~8 kilometers of each other and displayed a limited distribution within the Flagstaff area. However, in one case, closely related Y. pestis genotypes had spread between Williams, and Flagstaff, AZ, revealing the ability to disperse ~77 kilometers within three years. We also found examples of genomes sampled 10 years apart with no identified variation (n=0 SNPs), suggesting Y. pestis can persist with low replication levels through extended periods of time. This study has allowed us to identify local phylogenetic lineages of Y. pestis circulating near Flagstaff, AZ and follow their persistence for two decades.

• Publisher: ProQuest Dissertations & Theses
• Subject: Biology / Genetics / Microbiology
• ISBN: 9798382750880