Glossary

Acquisition event
The point at which a person or host becomes newly infected with a pathogen. In epidemiology, tracking acquisition events helps determine when and where transmission occurs.

Adenine
One of the four nucleotide bases found in DNA and RNA, often represented as “A.”

Artificial Intelligence (AI)
A technology that enables computers to make advanced calculations, solve problems, and provide recommendations at rapid speed. AI technologies such as large language models (LLMs) perform tasks that typically require human intelligence, such as visual perception, speech recognition, and decision-making.

Bacterial culture
A technique that involves growing bacteria in a laboratory in order to isolate, identify, or study organisms.

Bioinformatician
A scientist or specialist who develops or uses computational and statistical techniques to analyze biological data, such as DNA or RNA sequences.

Bioinformatics
An interdisciplinary field that combines biology, computer science, and mathematics to compile, process, and analyze large biological datasets, including genome sequences.

Case interview
A method used in epidemiology where patients may be asked questions about their illness, activities, exposures, and recent contacts. The information is used to help identify how the infection is spreading, such as the potential source or mode of transmission.

Chromatography
A laboratory technique used to separate mixtures of substances into their individual components, often used in microbiology and molecular biology for analyzing biological samples.

Contact tracing
A public health strategy that involves identifying and following up with people who have been exposed to a person with an infectious disease. The approach is used to clarify how infectious diseases are spreading and informs strategies to prevent further transmission.

Cytosine
One of the four nucleotide bases in DNA and RNA, represented as “C.”

Demographics
Statistical data relating to the characteristics of human populations, such as age, race, gender, or socioeconomic status. In public health, demographics can be used alongside epidemiological data to understand how different pathogens affect different groups and aid in designing appropriate interventions.

DNA (Deoxyribonucleic acid)
Deoxyribonucleic acid, the chains of nucleotides that carry genetic instructions for the biological functions, including development and reproduction, of almost all known organisms. DNA is primarily comprised of 4 nucleotide bases: adenine, cytosine, guanine, and thymine.

Epidemic
A sudden increase in cases of a particular disease affecting a large region, well above the level that might normally be expected in a community or region.

Epidemiologic investigation
A systematic process used by public health professionals to gather information and analyze data about infectious disease outbreaks or health events, with the aim of identifying sources of illnesses, transmission routes, and ways to control further spread.

Epidemiologist
A public health or research professional who studies patterns, causes, and effects of health and disease conditions in defined populations.

Epidemiology
The study of disease in populations to understand patterns in disease frequency and causes of those patterns, with the goal of improving population health. Epidemiology covers communicable and noncommunicable diseases, and data collected is used to inform interventions to prevent disease or strategies to manage existing diseases.

Evolution
The process by which organisms change over time, typically due to a combination of random genomic changes and selection.

Germ theory
The widely accepted scientific theory stating that infectious diseases are caused by microorganisms (such as bacteria, viruses, and fungi) that infect a host person or animal.

Genetic material
Nucleotides that carry genetic information that is responsible for the growth, survival, and other biological functions of living organisms. This could refer to a section of DNA or RNA or a complete blueprint (see genome).

Genome
The complete set of genetic material in an organism. The genome carries the instructions for building and maintaining the organism. See also: Genetic material.

Genome assembly
The process of piecing together DNA sequence fragments, such as the raw data from a sequencing instrument, to reconstruct the entire genome sequence of an organism. Alternatively, genome assembly can refer to the product of assembled genome fragments produced by genetic sequencing.

Genomic epidemiology
A subfield of epidemiology that analyzes genome sequences of pathogens (sometimes jointly with epidemiologic data) to detect and define outbreaks, explore pathogen transmission, and characterize pathogens (such as detecting antimicrobial resistance). Integrating genomic data with traditional epidemiological approaches provides detailed insights into outbreak origins and transmission pathways, informing more targeted public health interventions.

Genomic surveillance
In the context of public health, the systematic and ongoing collection, sequencing, and analysis of pathogen genomes from populations to monitor trends, track spread, and detect genetic changes in the pathogens in order to inform public health.

Guanine
One of the four nucleotide bases of DNA and RNA, symbolized as “G.”

Host
A person or animal that can be infected by a pathogen under natural conditions.

Immunologic methods
Laboratory techniques that use antibodies or other immune system components to detect or measure specific pathogens or other substances in a sample.

Machine learning
A subset of artificial intelligence that involves algorithms that can learn from and make predictions or decisions based on data.

Mass spectrometry
An analytical technique that measures the mass and composition of molecules, widely used to identify biological molecules, such as proteins, metabolites, or other chemicals in biological samples.

Microbe (or Microorganism)
An organism, such as a bacterium, virus, or fungus, that is too small to be seen without a microscope.

Microbiology
The scientific study of microorganisms, including their biology, classification, and roles in health and disease.

Miasma theory
An outdated scientific theory that attributed all infectious diseases to “bad air” or noxious forms of pollution, even those we now know are caused by microorganisms.

Molecular epidemiology
A subfield of epidemiology that uses the genetic material of disease-causing organisms to understand patterns of infectious disease occurrence and spread.

Mutation
A change in the genetic code of an organism that typically occurs during replication.

Nucleotide
A molecule consisting of a base (adenine, cytosine, guanine, or thymine/uracil) and some additional common structural elements. Nucleotides serve as the building blocks of DNA and RNA.

Outbreak
Refers to the occurrence of cases of a particular disease in a geographic area or population group at a higher frequency than would normally be expected.

Pandemic
An outbreak of an infectious disease occurring over a wide geographic area and affecting a significant proportion of the regional or global population.

Pathogen
A microorganism that has the potential to cause disease in its host. Major groups that can act as pathogens include viruses, bacteria, fungi, or protozoa.

Pathogen characterization
The process of identifying the specific features and properties of a pathogen, such as its type, genetic makeup, and how it causes disease.

Pathogen function
How a pathogen infects hosts, evades immune responses, or causes infectious disease. Changes in a pathogen's genome sequence can result in changes in pathogen function.

Pathogen genomics
The study of the genetic material of pathogens in order to understand their transmission, evolution, and potential for causing disease. Pathogen genomics can help inform public health efforts to control and treat infectious disease.

Pathogen identification
The process of determining which specific pathogen is present in a sample. It is done using laboratory techniques.

Pathogen particles
Refers to the complete form of a pathogen capable of causing infectious disease and transmitting the infectious agent between hosts. This term is pathogen-agnostic and can refer to viruses, bacteria, or fungi. The structure and composition of a pathogen particle vary depending on the type of pathogen. More specific terminology is generally used for known pathogens – for example, a viral pathogen particle is called a virion.

Pathogen subtyping
A further classification of pathogens beyond the species level, identifying subgroups with distinct genetic or biological characteristics.

Polymerase Chain Reaction (PCR)
A laboratory technique that rapidly amplifies specific segments of DNA, allowing for the detection and analysis of genetic material from pathogens in a sample.

Pulsed-Field Gel Electrophoresis (PFGE)
Often called 'DNA fingerprinting', PFGE refers to a laboratory method used to separate large DNA molecules by size; useful for comparing and distinguishing between strains of pathogens.

Ribonucleic acid (RNA)
Ribonucleic acid, a molecule similar to DNA that plays a critical role in coding, decoding, regulation, and expression of genes. Some viruses use RNA as their genetic material.

Sequencer
A laboratory instrument that determines the precise order of nucleotides (adenine, thymine, cytosine, and guanine) within the genetic material (DNA or RNA) of a sample. A sequencer could be used to sequence sections of genetic material from an organism, or the entire genetic material (genome) of an organism.

Sequencing
A laboratory procedure that determines the specific order of nucleotides in a section of DNA or RNA. This could be a section of genetic material for analysis, or the whole genome of an organism.

Sequencing data
The information generated from determining the order of nucleotides (DNA or RNA) in one or more genomes, such as those of pathogens. These data are derived from biological samples, which may be collected from infected individuals, the environment, or other sources.

Species
A group of organisms that share common characteristics, representing the most basic unit of biological classification.

Strain
A genetic variant or subtype of a microbial species (such as a virus or bacterium). Different strains may have unique characteristics.

Strain prevalence
The frequency or proportion of a particular strain of a pathogen within a population or sample at a specific time.

Surveillance
In the context of public health, the systematic and ongoing collection, analysis, and interpretation of health or disease data to inform public health action.

Thymine
One of the four nucleotide bases in DNA, denoted as “T.”

Transmission
In the context of infectious disease, refers to the process by which an infectious agent or pathogen is spread from one host to another.

Variant
In the context of infectious diseases and pathogens, a variant refers to a version of a microorganism—such as a virus, bacterium, or fungus—that has undergone genomic changes or mutations compared to the original or predominant version. These changes occur naturally over time as the pathogen replicates and spreads.