Talima Pearson

Northern Arizona University | NAU · Department of Biological Sciences

Genomic diversity in a pathogen population is the foundation for evolution and adaptations in virulence, drug resistance, pathogenesis, and immune evasion. Characterizing, analyzing, and understanding population-level diversity is also essential for epidemiological and forensic tracking of sources and revealing detailed pathways of transmission and...

Leptospirosis (caused by pathogenic bacteria in the genus Leptospira) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, such as rats, or a urine-contaminated environment, which then can serve as an infection source for additional rats...

Background Leptospirosis is the world’s most common zoonotic disease. Mitigation and control rely on pathogen identification and understanding the roles of potential reservoirs in cycling and transmission. Underreporting and misdiagnosis obscure the magnitude of the problem and confound efforts to understand key epidemiological components. Difficul...

Background Most seasonally circulating enteroviruses result in asymptomatic or mildly symptomatic infections. In rare cases, however, infection with some subtypes can result in paralysis or death. Of the 300 subtypes known, only poliovirus is reportable, limiting our understanding of the distribution of other enteroviruses that can cause clinical d...

Background Leptospirosis is the world’s most common zoonotic disease. Mitigation and control rely on pathogen identification and understanding the roles of potential reservoirs in cycling and transmission. Underreporting and misdiagnosis obscure the magnitude of the problem and confound efforts to understand key epidemiological components. Difficul...

Asymptomatic carriage of Staphylococcus aureus is a major risk factor for subsequent clinical infection. Diminishing returns from mitigation efforts emphasize the need to better understand colonization, spread, and transmission of this opportunistic pathogen. While contact with other people presents opportunities for pathogen exposure and transmiss...

Background: Leptospirosis causes significant economic losses and is an occupational risk in the swine industry, especially in developing tropical regions where social and geoclimatic conditions are favorable for the transmission of this disease. Although vaccination can reduce infection risk, efficacy is diminished if local genetic and antigenic v...

Staphylococcus aureus is a frequent cause of mild and severe infections that occur when these commensal bacteria penetrate the outer layers of skin or mucosa. As most S. aureus infections are the result of autoinfection, and community-acquired infections are increasingly common, it is important to better understand S. aureus colonization characteri...

Background Leptospirosis, caused by Leptospira bacteria, is a common zoonosis worldwide, especially in the tropics. Reservoir species and risk factors have been identified but surveys for environmental sources are rare. Furthermore, understanding of environmental Leptospira containing virulence associated genes and possibly capable of causing disea...

Background Leptospirosis causes significant economic losses and is an occupational risk in the swine industry, especially in developing tropical regions where social and geoclimatic conditions are favorable for the transmission of this disease. Although vaccination can reduce infection risk, efficacy is diminished if local genetic and antigenic var...

Background Leptospirosis, caused by Leptospira bacteria, is a common zoonosis worldwide more prevalent in the tropics. Reservoir species and risk factors have been identified but surveys for environmental sources of leptospirosis are rare. Furthermore, understanding of environmental Leptospira containing pathogenic genes and possibly capable of cau...

Staphylococcus aureus exists as a pathogen and commensal. Individuals with asymptomatic carriage serve as a reservoir for transmission and are at increased risk of infecting themselves. In order to characterize the genomic diversity of S. aureus circulating in the community, we sequenced 166 genomes collected from individuals in Yuma, AZ.

Background Molecular assays are important tools for pathogen detection but need to be periodically re-evaluated with the discovery of additional genetic diversity that may cause assays to exclude target taxa or include non-target taxa. A single well-developed assay can find broad application across research, clinical, and industrial settings. Patho...

Aims: To understand the impact of storage temperature on recovery of Staphylococcus aureus on sampling swabs. S. aureus is a common cause of skin and soft tissue infections, but also causes a variety of life-threatening diseases. With a large pool of asymptomatic carriers and transmission that can occur even through indirect contact, mitigation ef...

In this study we examined changes to the human gut microbiome resulting from an eight-week intervention of either cardiorespiratory exercise (CRE) or resistance training exercise (RTE). Twenty-eight subjects (21 F; aged 18–26) were recruited for our CRE study and 28 subjects (17 F; aged 18–33) were recruited for our RTE study. Fecal samples for gut...

Background Leptospira are shed into the environment via urine of infected animals. Rivers are thought to be an important risk factor for transmission to humans, though much is unknown about the types of environment or characteristics that favor survival. To address this, we screened for Leptospira DNA in two rivers in rural Ecuador where Leptospiro...

In the twenty-first century, ticks and tick-borne diseases have expanded their ranges and impact across the US. With this spread, it has become vital to monitor vector and disease distributions, as these shifts have public health implications. Typically, tick-borne disease surveillance (e.g., Lyme disease) is passive and relies on case reports, whi...

This study was carried out to evaluate hypotheses generated by fundamental cause theory regarding the socioeconomic status (SES) gradient in colonization with Staphylococcus aureus among Hispanic and non-Hispanic adults living in a border community. Participants ( n = 613) recruited in naturally occurring small groups at public and private sites th...

Streptococcus suis is primarily a pig pathogen and a zoonotic agent. Recently, the isolation of S. suis strain 10-36905 from a case of meningitis in cattle was reported. The draft genome sequence of this isolate demonstrates its divergent relationship with other S. suis strains.

Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this long-term symbiotic relationship to b...

Background: Pancreatic cancer remains a deadly disease, and immunotherapy is effective in only 1-2% of microsatellite instability-high pancreatic cancers. The response to immunotherapy is very heterogeneous across tumor types, but recently there is evidence that the gastrointestinal microbiome may influence the response to immunotherapy. The SU2C C...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

BACKGROUND Healthcare-associated (HA) Staphylococcus aureus (S. aureus) infections are declining but remain common. Conversely, rates of community-associated (CA) infections have not decreased due to the inadequacy of public health mechanisms to control transmission in a community setting. Our long-term objective is to use risk-based information fr...

Background Health care–associated Staphylococcus aureus infections are declining but remain common. Conversely, rates of community-associated infections have not decreased because of the inadequacy of public health mechanisms to control transmission in a community setting. Our long-term goal is to use risk-based information from empirical socio-cul...

Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where the disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this chronic infection to better under...

It has been previously reported that ursodeoxycholic acid (UDCA), a therapeutic bile acid, reduced risk for advanced colorectal adenoma in men but not women. Interactions between the gut microbiome and fecal bile acid composition as a factor in colorectal cancer neoplasia have been postulated but evidence is limited to small cohorts and animal stud...

Globalization has facilitated the worldwide movement and introduction of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans, a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has e...

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visua...

Burkholderia pseudomallei is the environmental bacillus that causes melioidosis; a disease clinically significant in Australia and Southeast Asia but emerging in tropical and sub-tropical regions around the globe. Previous studies have placed the ancestral population of the organism in Australia with a single lineage disseminated to Southeast Asia....

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visua...

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visua...

Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and island...

The Burkholderia pseudomallei isolate MSHR1435 is a fully virulent environmental sequence type 131 (ST131) isolate that is epidemiologically associated with a 17.5-year chronic melioidosis infection. The completed genome will serve as a reference for studies of environmental ecology, virulence, and chronic B. pseudomallei infections.

Objective We previously reported that Ursodeoxycholic acid (UDCA), a therapeutic bile acid, reduces risk for advanced colorectal adenoma in men but not women. Interactions between the gut microbiome and fecal bile acid composition as a factor in colon cancer neoplasia have been postulated but evidence is limited to small cohorts and animal studies....

of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans, a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has exhibited few genetic polymorphisms in previous studies, presenting cha...

Here, we report draft genome sequences of historical strains of Coxiella burnetii derived from cow’s milk and the placenta of a goat that had aborted. The California and Ohio milk strains display a different sequence type than do contemporary milk strains.

Leptospirosis after exposure to soil or water contaminated with urine of infected animals is the most common way in which humans contract the disease. Entire populations can be at high risk of leptospirosis after working in inundated fields, engaging in aquatic sports, or after periods of heavy rainfall. Risk of infection after contact with these e...

In 1998, it was claimed that an 80-year-old glass tube intentionally filled with Bacillus anthracis and embedded in a sugar lump as a WWI biological weapon still contained viable spores. Today, genome sequencing of three colonies isolated in 1998 and subjected to phylogenetic analysis surprisingly identified a well-known B. anthracis reference stra...

Compelling evidence suggests that gut flora influences colorectal cancer risk through direct effects on colonic bile acid composition. Bile acids are widely implicated in the etiology of colorectal cancer with the strongest evidence involving a detrimental role for the secondary BA, deoxycholic acid (DCA) and a protective effect of ursodeoxycholic...

Background Leptospirosis is a major zoonotic disease with widespread distribution and a large impact on human health. Carrier animals excrete pathogenic Leptospira primarily in their urine. Infection occurs when the pathogen enters a host through mucosa or small skin abrasions. Humans and other animals are exposed to the pathogen by direct contact...

Studies at the national level in the USA report high herd level prevalence of infection with Coxiella burnetii in dairy cattle while goats have been reported as the source of outbreaks of Q fever. However, trends at the national level may not always reflect the regional or local situation. As part of studies estimating the prevalence of C. burnetii...

Importance: The 1979 Russian anthrax outbreak resulted from an industrial accident at the Soviet anthrax spore production facility in the city of Sverdlovsk. Deep genomic sequencing of two autopsy specimens generated a draft genome and phylogenetic placement of the Soviet Sverdlovsk anthrax strain. While it is known that Soviet scientists had gene...

Healthcare-acquired infections (HAIs) kill tens of thousands of people each year and add significantly to healthcare costs. Multidrug resistant and epidemic strains are a large proportion of HAI agents, and multidrug resistant strains of Klebsiella pneumoniae , a leading HAI agent, have become an urgent public health crisis. In the healthcare envir...

Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is e...

Accession information for genomes screened in this study.

Locus tag information for the B. pseudomallei/mallei core genome.

Details of genomes sequenced in the current study.

Core genome regions across all B. pseudomallei genomes.

Background: Leptospirosis is a zoonotic disease responsible for high morbidity around the world, especially in tropical and low income countries. Rats are thought to be the main vector of human leptospirosis in urban settings. However, differences between urban and low-income rural communities provide additional insights into the epidemiology of t...

Supplementary File 1

Anthrax is a zoonotic disease that occurs naturally in wild and domestic animals but has been used by both state-sponsored programs and terrorists as a biological weapon. The 2001 anthrax letter attacks involved less than gram quantities of Bacillus anthracis spores while the earlier Soviet weapons program produced tons. A Soviet industrial product...

Compelling evidence suggests that the gut flora influences colorectal cancer risk through direct effects on colonic bile acid composition. Bile acids are widely implicated in the etiology of colorectal cancer and the strongest evidence is for the secondary bile acid deoxycholic acid. In a study of patients with prior colorectal adenomas who were ra...

Coxiella burnetii is a gram-negative bacterium that is the etiologic agent of the zoonotic disease Q fever. Common reservoirs of C. burnetii include sheep, goats, and cattle. These animals shed C. burnetii into the environment, and humans are infected by inhalation of aerosols. A survey of 1622 environmental samples taken across the United States i...

Q-fever is an underreported disease caused by the bacterium Coxiella burnetii, which is highly infectious and has the ability to disperse great distances. It is a completely clonal pathogen with low genetic diversity and requires whole-genome analysis to identify discriminating features among closely related isolates. C. burnetii, and in particular...

Pathogenic Leptospira spp. cause leptospirosis upon contact with mucosa through wounds or ingestion, leading to headaches, fever, jaundice, kidney or liver failure, or death in about 1.3 million people each year. Here, we present the draft genomes of one L. santarosai isolate and two L. interrogans isolates from Ecuador .

The insertion sequence IS1111 is used for molecular detection of Coxiella burnetii but also found in Coxiella-like endosymbionts of ticks, presenting a risk of false positive detection of C. burnetii. Limited IS1111 sequences from Coxiella-like bacteria restrict in silico assessment of IS1111 assays. However, Coxiella-like bacteria detectable by IS...

Supplementary Data

There have been two anthrax cases affecting people that played and/or made animal skin drums in the UK during the last ten years, with single fatal occurrences in Scotland in 2006 and London in 2008. Investigations by the Health Protection Agency (now Public Health England) employing Multi-Locus-Variable Number Tandem Repeat Analysis had previously...

PCR Primer Table.

Supplementary material.

Strains Table.

SNP Genotype Matrix.

VNTR Genotype Matrix.

Background: Anthrax is a rare disease in humans but elicits great public fear because of its past use as an agent of bioterrorism. Injectional anthrax has been occurring sporadically for more than ten years in heroin consumers across multiple European countries and this outbreak has been difficult to trace back to a source. Methods: We took a molec...

Coxiella burnetii is the etiologic agent of Q fever, a zoonotic disease causing influenza-like illness, pregnancy loss, cardiovascular disease and chronic fatigue syndrome in people. C. burnetii is considered to be enzootic in ruminants, but clinical signs of infection do not always manifest. National studies have documented the presence of C. burn...

Staphylococcus aureus is an important clinical pathogen worldwide and understanding this organism's phylogeny and, in particular, the role of recombination, is important both to understand the overall spread of virulent lineages and to characterize outbreaks. To further elucidate the phylogeny of S. aureus, 35 diverse strains were sequenced using w...

Twelve Burkholderia pseudomallei isolates collected over a 32-month period from a patient with chronic melioidosis demonstrated identical multilocus sequence types (STs). However, whole-genome sequencing suggests a polyclonal infection. This study is the first to report a mixed infection with the same ST.

Unlabelled: For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome s...

For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome sequence typin...

Author Summary Glanders is a disease of antiquity, recognized as a malady of equines by Hippocrates and Aristotle. The causative agent, Burkholderia mallei , is currently feared as a potential biological weapon and has been used as such in the American Civil War and both World Wars to cripple equine military components. In the more economically de...

The Bacillus anthracis strain STI is a Soviet vaccine strain that lacks the pXO2 plasmid. Previous data indicate that this isolate forms a new branch within the B. anthracis sub-group originally identified as A. Br.008/009.

We investigated a Q fever outbreak with human patients showing high fever, respiratory tract symptoms, headache and retrosternal pain in southern Hungary in the spring and summer of 2013. Seventy human cases were confirmed by analysing their serum and blood samples with micro-immunofluorescence test and real-time PCR. The source of infection was a...

Sequence analyses and subtyping of Bacillus anthracis strains from Georgia reveal a single distinct lineage (Aust94) that is ecologically established. Phylogeographic analysis and comparisons to a global collection reveals a clade that is mostly restricted to Georgia. Within this clade, many groups are found around the country, however at least one...

Background Information about the genotypic characteristic of Coxiella burnetii from Hungary is lacking. The aim of this study is to describe the genetic diversity of C. burnetii in Hungary and compare genotypes with those found elsewhere. A total of 12 samples: (cattle, n = 6, sheep, n = 5 and human, n = 1) collected from across Hungary were studie...

We used whole-genome analysis and subsequent characterization of geographically diverse strains using new genetic signatures to identify distinct subgroups within Francisella tularensis subsp. tularensis group A.I: A.I.3, A.I.8, and A.I.12. These subgroups exhibit complex phylogeographic patterns within North America. The widest distribution was ob...

Francisella tularensis whole-genome sequencing data generation, assembly, and analysis.

Coxiella burnetii causes Q fever in humans and Coxiellosis in animals; symptoms range from general malaise to fever, pneumonia, endocarditis and death. Livestock are a significant source of human infection as they shed C. burnetii cells in birth tissues, milk, urine and feces. Although prevalence of C. burnetii is high, few Q fever cases are report...