Click the topics below to see some defined terms and concepts that appear throughout our site.

Pathogens and Diseases

Acute flaccid myelitisa rare and serious neurological condition that causes weak muscles and reflexes, most commonly in young children
Antimicrobial resistance (AMR)a phenomenon that occurs over time when viruses, bacteria, and fungi develop mutations that allow them to survive despite treatment with medications; mutations occurs naturally but true resistance is often driven by misuse of antimicrobial agents
Apophysomycesa fungus found naturally in soils that can cause rare and oftentimes fatal infections; the only known outbreak followed exposure to a massive tornado in Joplin, MO
Bacillus cereusan environmental, foodborne bacterium that produces toxins in infected food, which may cause vomiting and diarrheal symptoms upon ingestion
Bordetella pertussisthe bacterial agent that causes pertussis (whooping cough), a highly contagious yet vaccine-preventable disease
Coccidioidesa fungal genus comprised of two species primarily found in soils of the North American Southwest, both of which infect the host through inhalation of spores and is the causative agent of Valley Fever; see Valley Fever
Cryptococcusan invasive environmental fungus that infects the host through inhalation of spores or yeast; inhaled fungus can cause cryptococcosis, a disease most often found in immunocompromised individuals that largely affects the lungs and nervous system
ESKAPE pathogensa category of six pathogens (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) that display resistance to multiple antimicrobial agents and are often spread in healthcare facilities
EV-D68a respiratory and enteric enterovirus that is known to  cause a rare polio like-disease known as acute flaccid myelitis; see Acute flaccid myelitis
Fungal meningitisa neurologic disease that can occur when a fungal infection spreads to the brain and spinal cord
Group A Streptococcusa bacteria (also called Streptococcus pyogenes) that can cause diseases such as strep throat, scarlet fever, and necrotizing fasciitis (i.e., flesh eating bacteria)
H1N1one of the two main types of human influenza viruses, both of which spread via respiratory droplets that can cause seasonal flu symptoms or more severe disease; H1N1 can recombine with other viruses (i.e., from pigs and birds), which led to the 2009 “swine flu” pandemic
Methicillin-resistant Staphylococcus aureus (MRSA)an infection caused by bacterium Staphylococcus aureus that has developed resistance to multiple antibiotics, making it difficult to treat
Onchocercaa genus of parasites including Onchocerca lupi, a parasitic worm that causes canine river blindness in the U.S.; the diseases is spread via biting flies
Pseudomonasa genus of bacteria, including Pseudomonas aeruginosa, a common cause of healthcare-associated infections
Salmonella entericaa common bacterium that is excreted in the feces of infected humans and animals, which can then spread in unclean water or contaminated food, eventually causing diarrheal illness
Sarocladium kiliensean opportunistic environmental fungus with high resistance to most antifungal treatments that can cause severe systemic infections in humans
SARS-CoV-2the causative agent of the Covid-19 pandemic; infection usually causes mild respiratory symptoms in most individuals, but can lead to serious illness and death in high risk populations
Tick-borne relapsing fevera disease in the western United States; caused by a spirochete bacterium that is acquired from the bite of a tick, typically in caves or rustic cabin settings; recurring symptoms include fever and headache
Tuberculosisthe number-one infectious disease killer in humans; spread via respiratory aerosols that primarily affect the lungs; extremely drug-resistant (XDR) strains are increasing
Valley Fevera fungal disease, primarily in the American Southwest, caused by inhalation of Coccidioides spores; symptoms include cough, fever, and fatigue and can often be treated with antifungals
West Nile Virusa bloodborne virus spread by the bite of an infected mosquito; infections range from asymptomatic to severe and deadly encephalitis or meningitis; no vaccine or medication treatment exists

Significant Terms

Amplicona section of genetic material that has been replicated to make millions of copies so that the amplified sequence can be closely studied; amplicons are commonly produced via polymerase chain reaction (PCR); see Polymerase chain reaction (PCR)
Bioinformaticsa scientific field that encompases both biology and computational science to handle, analyze, and visualize biological data
Genomic epidemiologythe use of genomic data to characterize the distribution and spread of infectious disease which can then be used to inform public health and health care interventions
Heteroresistancea mixture of subpopulations of antibiotic-resistant bacteria among antibiotic-susceptible bacteria of the same species
Isolatea pure culture of microbes derived from a mixed microbial community that is separated and grown on its own
Lineagea genetically closely related group of isolates within a microbial species derived from a common ancestor
Metagenomicsthe study of the totality of genetic material extracted from a clinical or environmental sample that may contain multiple microbial communities along with host genetic data
Microbiomethe ecosystem of all microbes that naturally live on and inside humans or the environment, including both pathogenic and beneficial bacteria, viruses, parasites, and fungi
Phylogeographicthe study of the relationship between spatial distribution (geography) and phylogeny (relatedness) of strains which can be used to further understand populations of microbes
SMORan acronym for Single Molecule Overlapping Reads; a type of next-generation sequence analysis that can identify the presence of very low level heteroresistance and other subpopulations; see Heteroresistance
SNPan acronym for Single-Nucleotide Polymorphism; a mutation that substitutes one nucleotide for another within a DNA or RNA sequence
Straina variant of a species with genetic, biological, or geographic differences that separate it from other variants of the same species
Varianta lineage of a microbe that has one or more stable mutations that differentiate it from other lineages within a species
Virulencethe relative ability of a microbe to cause disease in a host

Techniques and Tools

Genomic surveillancea method that uses genomic sequencing to monitor pathogen dynamics and disease trends in specific populations with an ami to identify important health events
Genotypinga technique or method that is used differentiating organism lineages based on detecting and measuring specific genomic characteristics (e.g., 16S gene sequence typing)
Next-generation sequencing (NGS)an approach that sequences millions of small DNA fragments and then uses bioinformatics to combine them into larger genomic pieces
Nucleic acid extractionthe isolation, purification, and concentration of nucleic acids (RNA and DNA) for downstream analysis
Phenotypinga technique or method that is used to differentiate organism lineages based on detecting and measuring specific biological characteristics (e.g., serotyping)
Phylogenetic analysisa biological tool for understanding and visualizing evolutionary history and organism relatedness over time and space based on genomic similarity
Phylogenetic treea diagram that depicts evolutionary history and relatedness among organisms or genes based on shared characteristics
Polymerase chain reaction (PCR)a laboratory technique that replicates DNA sequences of interest to be used in downstream analyses
Metagenomic sequencinga next-generation sequencing approach that allows for sequencing of a sample containing genetic material from more than one organism; see Next-generation sequencing
Wastewater surveillancethe use of detection methods to identify and quantify microbes and chemicals that have been shed in human or animal waste; this can provide early warning of disease outbreaks, especially when many individuals are asymptomatic
Whole genome sequencing (WGS)a comprehensive sequencing approach of a single organism’s genetic material that, after bioinformatic analysis, reveals an organism’s entire genome