Click the topics below to see some defined terms and concepts that appear throughout our site.
Pathogens and Diseases
| Acute flaccid myelitis | a 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 |
| Apophysomyces | a 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 cereus | an environmental, foodborne bacterium that produces toxins in infected food, which may cause vomiting and diarrheal symptoms upon ingestion |
| Bordetella pertussis | the bacterial agent that causes pertussis (whooping cough), a highly contagious yet vaccine-preventable disease |
| Coccidioides | a 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 |
| Cryptococcus | an 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 pathogens | a 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-D68 | a respiratory and enteric enterovirus that is known to cause a rare polio like-disease known as acute flaccid myelitis; see Acute flaccid myelitis |
| Fungal meningitis | a neurologic disease that can occur when a fungal infection spreads to the brain and spinal cord |
| Group A Streptococcus | a bacteria (also called Streptococcus pyogenes) that can cause diseases such as strep throat, scarlet fever, and necrotizing fasciitis (i.e., flesh eating bacteria) |
| H1N1 | one 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 |
| Onchocerca | a 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 |
| Pseudomonas | a genus of bacteria, including Pseudomonas aeruginosa, a common cause of healthcare-associated infections |
| Salmonella enterica | a 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 kiliense | an opportunistic environmental fungus with high resistance to most antifungal treatments that can cause severe systemic infections in humans |
| SARS-CoV-2 | the 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 fever | a 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 |
| Tuberculosis | the number-one infectious disease killer in humans; spread via respiratory aerosols that primarily affect the lungs; extremely drug-resistant (XDR) strains are increasing |
| Valley Fever | a 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 Virus | a 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
| Amplicon | a 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) |
| Bioinformatics | a scientific field that encompases both biology and computational science to handle, analyze, and visualize biological data |
| Genomic epidemiology | the 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 |
| Heteroresistance | a mixture of subpopulations of antibiotic-resistant bacteria among antibiotic-susceptible bacteria of the same species |
| Isolate | a pure culture of microbes derived from a mixed microbial community that is separated and grown on its own |
| Lineage | a genetically closely related group of isolates within a microbial species derived from a common ancestor |
| Metagenomics | the 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 |
| Microbiome | the ecosystem of all microbes that naturally live on and inside humans or the environment, including both pathogenic and beneficial bacteria, viruses, parasites, and fungi |
| Phylogeographic | the study of the relationship between spatial distribution (geography) and phylogeny (relatedness) of strains which can be used to further understand populations of microbes |
| SMOR | an 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 |
| SNP | an acronym for Single-Nucleotide Polymorphism; a mutation that substitutes one nucleotide for another within a DNA or RNA sequence |
| Strain | a variant of a species with genetic, biological, or geographic differences that separate it from other variants of the same species |
| Variant | a lineage of a microbe that has one or more stable mutations that differentiate it from other lineages within a species |
| Virulence | the relative ability of a microbe to cause disease in a host |
Techniques and Tools
| Genomic surveillance | a method that uses genomic sequencing to monitor pathogen dynamics and disease trends in specific populations with an ami to identify important health events |
| Genotyping | a 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 extraction | the isolation, purification, and concentration of nucleic acids (RNA and DNA) for downstream analysis |
| Phenotyping | a technique or method that is used to differentiate organism lineages based on detecting and measuring specific biological characteristics (e.g., serotyping) |
| Phylogenetic analysis | a biological tool for understanding and visualizing evolutionary history and organism relatedness over time and space based on genomic similarity |
| Phylogenetic tree | a 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 sequencing | a next-generation sequencing approach that allows for sequencing of a sample containing genetic material from more than one organism; see Next-generation sequencing |
| Wastewater surveillance | the 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 |