Abstract
Diagnosis of disease is a process of hypothesis, investigation, and synthesis. Regardless of whether a human, animal, or plant is afflicted, the process of diagnosis is strikingly similar. Positioned on the biosecurity continuum between surveillance and response, early and accurate diagnosis is critical to effective mitigation and management of disease. Infectious diseases have the potential to spread among animal or plant populations, jump species barriers, and result in epidemics and global pandemics. Additionally, zoonotic infectious agents can also significantly impact human health on a mass scale. It is critical that infectious diseases be identified and detected in a timely fashion to prevent spread. This chapter will delve into the resources and supporting activities for that process, demonstrated via case studies from animal and plant systems, illuminating similarities and differences in the diagnostic process tools that can be mobilized and enhanced for biosecurity.
TopIntroduction
At its most basic level, diagnostics is the process of figuring out what is causing a problem so that a solution can be prescribed. In humans, this might entail visiting a family physician who listens to a patient’s description of the problem and symptoms, observes the signs, orders a test swab of throat and nasal passages, and then concludes that the patient has a bacterial sinus infection. The patient then receives a prescription for rest, to support the body’s immune system response, and antibiotics, to kill the bacteria causing the current infection. The process deployed by the physician included collection of information from the patient and synthesis of those observations with data from tests as well as education in human medicine and knowledge of current diseases spreading in their community. Animal and plant practitioners use the same process, and even many of the same tools, for the benefit of farmers, ranchers, gardeners, and pet owners, all with the end goal of healthy plants and animals.
Diagnosis of disease is a process of hypothesis, investigation, and synthesis that encompasses hard science skills of investigation and testing hypotheses, as well as soft skills of conversation and imagination. Regardless of whether a human, animal, or plant is afflicted, the process of diagnosis is strikingly similar, even if the occasional term is different. For example, in plant diagnostics, symptoms are the observable plant response to disease, while signs are the evidence of the causal agents, but in human diagnostics, symptoms are what the patient reports, while signs are anything the clinician observes. Since these terms are often used interchangeably in practice, the authors will hew towards the animal and human practitioner for this chapter. Positioned on the biosecurity continuum between surveillance and response, early and accurate diagnosis is critical to effective mitigation and management of disease. The authors will focus on the diagnosis of infectious diseases in plants and animals. Infectious diseases have the potential to spread among animal or plant populations, jump species barriers and result in epidemics and global pandemics (Dhama, 2020; Lau, 2015; Lau, 2017; Mahy, 2000; Marano, 2007; Riedel, 2006; Wong, 2007). These can potentially cause severe economic losses to associated industries at a local or global scale. Additionally, zoonotic infectious agents can also significantly impact human health on a mass scale (Marano, 2007). It is critical that infectious diseases be identified and detected in a timely fashion to prevent spread. Diagnostic methods may be as simple as observing unique clinical signs or as complicated as employing advanced and cutting-edge technologies such as whole genome sequencing, metagenome-based diagnostics etc. This chapter will delve into the resources and supporting activities for that process, demonstrated via case studies from animal and plant systems. The authors will focus on the agricultural systems served by diagnosticians, illuminating similarities and differences in the diagnostic process tools that can be mobilized and enhanced for biosecurity.
Key Terms in this Chapter
Laboratory Information Management System (LIMS or LIS): Software used to capture, maintain, and transmit information pertaining to the specimens submitted to the laboratory, testing performed and the results of those tests and to disseminate a report of those results. A LIMS may also include financial functionality to support calculating fees for testing, sending invoices to clients and tracking accounts receivable.
Antigen: A foreign substance or organism, in whole or in part, capable of eliciting an immune response such as antibody production.
Polymerase Chain Reaction (PCR): A molecular test method utilizing an enzyme to rapidly make copies of DNA or RNA, usually coupled with a mechanism to specifically target and identify the nucleic acid sequence of a known pathogen.
Biomarker: A measurable substance in an organism whose presence is indicative of response to some phenomenon such as disease, infection, or environmental exposure.
ELISA: Acronym for enzyme-linked immunosorbent assay, a test method generally used to detect antibodies in serum or other fluid samples, but may also be built to detect antigens.
Proficiency Testing: Determining the competence of an individual or laboratory to correctly perform a test, usually done by having the individual or laboratory run the test on a carefully constructed set of samples that they do not know the true status of (blinded) and comparing their answers with the known true status of the samples as determined by a reference laboratory.
Whole Genome Sequencing (WGS): Determining the sequence of amino acids for the entirety of the genetic material of an organism.
STEM: Acronym for science, technology, engineering, and mathematics areas of knowledge.
Metagenomics: The study of a collection of genetic material (genomes) from a mixed community of organisms.
Phytosanitary/Sanitary Rules: Rules and regulations governing the health status of plants (phytosanitary) or animals (sanitary) in commerce.
Serological: Testing method utilizing serum or occasionally plasma, usually to detect antibodies or other biomarkers, occasionally to detect antigen.
Triage: Performing an initial assessment of a situation or clinical submission and deciding what further course of action is warranted to best serve the diagnostic needs of the case.
Morphology: The gross physical appearance of an organism.
Multiplexing: An assay design that allows for the detection of multiple targets, usually representing multiple pathogens or biomarkers, at the same time.
Pathophysiology: The effect(s) of a pathogen on the normal functioning (physiology) of the host plant or animal.
Gene Sequencing: A method of determining the order and number of amino acids that make up the chain of a genetic molecule or gene, which provides a unique identification (DNA or RNA).
Zoonotic: A disease capable of being transmitted between animals and humans, in either direction.
Molecular: Testing method based on detection of nucleic acids (DNA or RNA).
Forensic(s): The science of investigation and diagnosis of the cause(s) of death or injury in criminal or legal cases.
Pathogen: An organism capable of causing clinical disease in a host.
Antibody: A molecule produced by an organism in response to the presence of a foreign substance, organism (bacteria, virus, fungus) or antigen as a defensive mechanism.