Andres Sebastian Espindola

Andres Sebastian Espindola
Oklahoma State University - Stillwater | Oklahoma State · Institute of Biosecurity and Microbial Forensics

PhD. Plant Pathology
Bioinformatics and high-throughput sequencing for microbial detection

About

36
Publications
7,351
Reads
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211
Citations
Additional affiliations
January 2017 - December 2020
Oklahoma State University - Stillwater
Position
  • PostDoc Position
August 2015 - December 2015
Oklahoma State University - Stillwater
Position
  • Graduate Teaching Assistant
Description
  • Principles of Plant Pathology: Basic concepts and principles of plant pathology and their influence in disease management.
August 2014 - December 2014
Oklahoma State University - Stillwater
Position
  • Graduate Teaching Assistant
Description
  • Principles of Plant Pathology: Basic concepts and principles of plant pathology and their influence in disease management.

Publications

Publications (36)
Article
Full-text available
The validation of diagnostic assays in plant pathogen detection is a critical area of research. It requires the use of both negative and positive controls containing a known quantity of the target pathogen, which are crucial elements when calculating analytical sensitivity and specificity, among other diagnostic performance metrics. High Throughput...
Article
Full-text available
Introduction. With expanding demand for diagnostics, newer methodologies are needed for faster, user-friendly and multiplexed pathogen detection. Metagenome-based diagnostics offer potential solutions to address these needs as sequencing technologies have become affordable. However, the diagnostic utility of sequencing technologies is currently lim...
Article
Full-text available
Sequence-based approaches and detection technologies have revolutionized plant disease diagnostics in the last few decades, opening the door to highly selective and specific diagnostic assays. However, diagnostic assay development and validation remains hindered by many factors, which would be ameliorated by research prioritization and coordination...
Article
Full-text available
The blueberry industry, a fast-growing industry in Florida, is threatened by bacterial wilt, caused by the Ralstonia solanacearum species complex (RSSC). In 2016, distinct RSSC populations were found in Florida causing disease in blueberry. Currently, there are no tools that discriminate between RSSC populations pathogenic to blueberry and other RS...
Article
Full-text available
The cost for high-throughput sequencing (HTS) has decreased significantly and has made it possible for the application of this technology for routine plant diagnostics. There are constraints to the use of HTS as a diagnostic tool, including the need for dedicated personnel with a bioinformatic background for data analysis and the lack of a standard...
Article
Full-text available
Species identification of plant pathogenic oomycetes based on morphology is challenging because of the limited number of variable characters available. Hence, pure culture isolation followed by internal transcribed spacer sequencing is routinely conducted for diagnostic purposes. E-probe Diagnostic Nucleic acid Analysis (EDNA), a pipeline that coup...
Article
The advancement in high-throughput sequencing (HTS) technology allows the detection of pathogens without the need for isolation or template amplification. Plant regulatory agencies worldwide are adopting HTS as a pre-screening tool for plant pathogens in imported plant germplasm. The technique is a multipronged process, and often the bioinformatic...
Chapter
E-probe Diagnostic for Nucleic Acid Analysis (EDNA) is a user-friendly bioinformatic tool that has been adapted for the detection and identification of citrus exocortis viroid (CEVd). Here, we describe the procedures for RNA extraction from citrus tissues, library and sequencing preparation, and the utilization of EDNA Mi-Finder online platform on...
Article
Full-text available
High-throughput sequencing (HTS) is becoming the new norm of diagnostics in plant quarantine settings. HTS can be used to detect, in theory, all pathogens present in any given sample. The technique’s success depends on various factors, including methods for sample management/preparation and suitable bioinformatic analysis. The Limit of Detection (L...
Article
Full-text available
Background Spiroplasma citri comprises a bacterial complex that cause diseases in citrus, horseradish, carrot, sesame, and also infects a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean...
Article
Full-text available
Agricultural high throughput diagnostics need to be fast, accurate and have multiplexing capacity. Metagenomic sequencing is being widely evaluated for plant and animal diagnostics. Bioinformatic analysis of metagenomic sequence data has been a bottleneck for diagnostic analysis due to the size of the data files. Most available tools for analyzing...
Article
Gut microbiota play an important role in extraction, synthesis and absorption of nutrients. Commensal bacteria prevent pathogenic bacteria colonization and maintain intestinal epithelium integrity. The most common families of commensal bacteria in nursery pigs are Prevotellaceae, Clostridiaceae, Erysipelotrichaceae, Lachnospitaceae, Lactobacillacea...
Preprint
Full-text available
Background Spiroplasma citri comprises a complex of bacteria that cause diseases in citrus, horseradish, carrot, sesame, and also infect a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean...
Preprint
Full-text available
Background Spiroplasma citri comprises a complex of bacteria that cause diseases in citrus, horseradish, carrot, sesame, and also infect a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean...
Article
Full-text available
Coniothyrium glycines , the causal agent of red leaf blotch in soybeans, is considered a high-consequence biological agent. With limited genomic information known, there are no molecular genotyping or detection methods available. We report the draft genome sequences of three C. glycines isolates, greatly enhancing our knowledge of this species.
Article
Full-text available
Coniothyrium glycines, the causal agent of red leaf blotch in soybeans, is considered a high-consequence biological agent. With limited genomic information known, there are no molecular genotyping or detection methods available. We report the draft genome sequences of three C. glycines isolates, greatly enhancing our knowledge of this species.
Article
Full-text available
A brief description of a few amenable technologies developed for research in biomedical and agricultural diagnostics tested using plant pathogens as microbial surrogates are presented. Plant pathogen surrogate microbes can assist in easing compliance with regulations and reducing costs, ethical and biosafety concerns in biomedical research.
Article
Full-text available
Ralstonia solanacearum is the causal agent of bacterial wilt in numerous species of plants. Here, we report the whole-genome sequence of three phylogenetically diverse R. solanacearum strains, P816, P822, and P824, reported for the first time as causal agents of an emerging blueberry disease in Florida.
Article
Full-text available
E-probe Diagnostic for Nucleic acid Analysis (EDNA) is a bioinformatic tool originally developed to detect plant pathogens in metagenomic databases. However, enhancements made to EDNA increased its capacity to conduct hypothesis directed detection of specific gene targets present in transcriptomic databases. To target specific pathogenicity factors...
Data
Expression values (log2 fold change) for AF70 A. flavus strain for two culture conditions (ground corn and PDB). For each Gene ID, expression levels are listed along with p-values. (XLSX)
Conference Paper
Full-text available
Aspergillus flavus is a major food safety concern for the food industry. Toxic strains produce varying amounts of the carcinogen aflatoxin B1. This study aims to improve the time-consuming soil sampling, isolation, culturing, toxin detection and exploration of the soil microbiome needed to manage aflatoxin contamination. Third Generation Sequencing...
Preprint
Full-text available
E-probe Diagnostic for Nucleic acid Analysis (EDNA) is a bioinformatic tool originally developed to detect plant pathogens in metagenomic databases. However, enhancements made to EDNA increased its capacity to conduct hypothesis directed detection of specific gene targets present in transcriptomic databases. To target specific pathogenicity factors...
Article
Early stage infections caused by fungal/oomycete spores may not be detected until signs or symptoms develop. Serological and molecular techniques are currently used for detecting these pathogens. Next-generation sequencing (NGS) has potential as a diagnostic tool, due to the capacity to target multiple unique signature loci of pathogens in an infec...
Article
Early stage infections caused by fungal/oomycete spores may not be detected until signs or symptoms develop. Serological and molecular techniques are currently used for detecting these pathogens. Next-generation sequencing (NGS) has potential as a diagnostic tool, due to the capacity to target multiple unique signature loci of pathogens in an infec...
Article
Full-text available
Phymatotrichopsis omnivora, the causal pathogen of cotton root rot, is a devastating ascomycete that affects numerous important dicotyledonous plants grown in the southwestern United States and northern Mexico. P. omnivora is notoriously difficult to isolate from infected plants; therefore methods for accurate and sensitive detection directly from...
Article
Plant biosecurity requires rapid identification of pathogenic organisms. While there are many pathogen-specific diagnostic assays, the ability to test for large numbers of pathogens simultaneously is lacking. Next generation sequencing (NGS) allows one to detect all organisms within a given sample, but has computational limitations during assembly...
Article
Full-text available
El arsénico (As) es un elemento químico que está en la naturaleza en distintas formas; muy pocas veces se lo encuentra en forma sólida y se lo puede hallar en plantas y animales en su forma orgánica que es la menos tóxica. La mayoría de las veces el arsénico se combina con el oxígeno, cloro y azufre para formar compuestos inorgánicos de arsénico qu...

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