Glossary
agar: An inert gelatin-like substance that provides a solid surface for growth of microbial colonies.
amino acid: One of 20 small molecules that comprise the subunits of proteins.
amino acyl tRNA synthetase: An enzyme that attaches a specific type of amino acid to a specific type of transfer RNA in preparation for protein synthesis; each amino acid-tRNA combination uses a different amino acyl tRNA synthetase.
antibiotic: A chemical that controls infection by blocking microbial growth and, in some cases, by killing microbes while doing little harm to the mammalian host of the microbes; in Antibiotic Resistance, antibiotics are considered to include antibacterial, antiviral, antifungal, antiprotozoan, and antihelminth agents.
antibiotic resistance: The capability of a particular pathogen population to grow in the presence of a given antibiotic when the antibiotic is used according to a particular regimen. See clinical resistance.
antigen: A chemical group recognized by an antibody.
antisense oligonucleotides: Short single-stranded DNA molecules designed to hybridize to specific nucleic acid targets.
antiseptic: A chemical that kills microbes but is safe enough to be applied to human skin.
Area Under the Curve (AUC): A measure of antibiotic concentration over time; determined by plotting concentration versus time and then measuring the area under that plot.
bacteriophage: Virus that infects bacteria.
bacterium: A single-celled organism that reproduces by binary fission and lacks a true nucleus, mitochondrion, or chloroplast.
base pair: Two nucleotides, each in a different strand of DNA, that interact; generally as complementary base pairs such that A pairs with T or U and G pairs with C.
bioavailability: The degree to which or rate at which an antibiotic is absorbed or becomes available at the site of physiological activity.
biofilm: A complex aggregation of microbes growing on a solid surface, often exhibiting reduced susceptibility to antibiotics.
breakpoint: (interpretative breakpoint) A value of MIC that correlates with antibiotic failure; when an isolate has an MIC above the breakpoint, it is considered to be resistant.
broad-spectrum antibiotic: Having activity against many pathogen species.
CA-MRSA: Community-associated, methicillin-resistant Staphylococcus aureus, a common cause of skin and soft-tissue infections outside hospitals or other institutions.
cassette integration: A process by which genes are moved and assembled by an integron.
chain termination: A process in which incorporation of an “abnormal” nucleoside into DNA blocks further DNA synthesis; many antiviral agents act by chain termination.
chromosome: Large DNA molecule that contains nucleotide sequence information specifying properties of an organism.
clinical resistance: A situation in which the MIC of an isolate is above the interpretative breakpoint.
clone (noun): A group of cells that have all descended from the same cell.
codon: Nucleotide triplet in DNA and mRNA that corresponds to a specific amino acid in protein.
codon usage: The bias exhibited by an organism for use of a particular set of tRNAs and their corresponding codons in protein synthesis; two regions of DNA having different codon usage are thought to have different evolutionary origins.
colony: A visible growth on a solid surface arising from multiple rounds of microbial reproduction.
commensal: An organism benefited by the presence of another organism without affecting the second organism.
complementary base pair: Two nucleotides, each in a different strand of DNA, that interact such that A pairs with T or U and G pairs with C.
confluent growth: A situation occurring with cultured animal cells in which the cells stop growing and dividing when they touch each other; the result is a layer of cells one-cell thick on the bottom of a Petri dish.
conjugation: The process by which DNA is actively passed from one microbial cell to another; with bacteria, conjugation generally involves a plasmid.
cross resistance: A resistance mechanism that applies to two or more antibiotics; an example is drug efflux in which resistance is conferred to multiple antibiotics.
cytokine: A member of a family of polypeptide regulators of the immune response; an example is interferon.
Directly Observed Therapy (DOT): A procedure in which healthcare workers visit tuberculosis patients to assure that the patients take the prescribed antibiotics.
disinfectant: A chemical that kills microbes and is generally applied to inanimate surfaces.
DNA: Deoxyribonucleic acid; a long, thin, chain-like molecule that contains the information for nucleotide sequences of RNA molecules and amino acid sequences of proteins.
DNA duplex: Double-strand DNA.
DNA polymerase: An enzyme complex that makes new DNA molecules by adding nucleotides one at a time to the end of a growing DNA molecule using a complementary DNA strand as a template.
DNA replication: Synthesis of DNA.
DNA virus: A virus that uses DNA as its genetic material.
efflux pump: A set of proteins that work together to expel antibiotics and other small molecules from cells.
empiric therapy: Use of antibiotics to treat disease without laboratory tests to identify the caustive pathogen or to determine its antibiotic susceptibility.
enzyme: A macromolecule, usually protein, that accelerates a chemical reaction without being consumed by the reaction.
eukaryotic: A type of organism that has a true nucleus and generally other organelles.
Extensively Drug Resistant (XDR): A strain of pathogen resistant to most available antibiotics; with M. tuberculosis, XDR means resistance to isoniazid, rifampicin, a fluoroquinolone, and one injectable drug (capreomycin, amikacin, or kanamycin).
fitness: A measure of the capability of an organism to grow and survive in a particular environment.
focus (noun): A pile of animal cells generated by infection with a tumor virus that prevents the cells from ceasing growth when they touch other cells.
fungus: A type of eukaryotic organism characterized by having a cell wall but lacking chloroplasts; examples are yeast, molds, and mushrooms.
gene mobilization: A process by which a chromosomal gene is transferred to a plasmid that then transfers the gene to other bacterial cells.
general recombination: See homologous recombination.
generalized transduction: Movement of bacterial genes from one bacterial cell to another by a bacteriophage such that any gene can be moved.
genome: The information content (nucleotide sequence) of an organism.
genomic island: A region of nucleotides in the genome of an organism in which the AT to GC ratio and/or codon usage in the region is different from the bulk of the genome, suggesting that the region of nucleotides had an origin different from the bulk of the genome.
growth promoter: Antibiotic administered at low doses to food animals to enhance animal growth.
HA-MRSA: Hospital-associated methicillin-resistant Staphylococcus aureus, a common cause of serious infections in hospitals and other institutions.
high throughput screening: A process in which large numbers of molecules are tested for activity, generally using robotics for sample testing.
homologous recombination: Breakage and rejoining of DNA regions of similar (homologous) nucleotide sequence such that two DNA molecules exchange regions.
horizontal transfer: Movement of genes from one microbial cell to another, as opposed to inheritance of genes from mother cell to daughter cell.
hydroxyl radical: A small, highly reactive molecule composed of an oxygen, a hydrogen, and an excess electron (neutral form of hydroxyl ion); considered to be a reactive oxygen species.
inflammation: A complex response of a host to injury or infection in which leukocytes and plasma move from the blood to the injured region.
insertion site: Location in a DNA molecule where another DNA molecule inserts (integrates); often recognized by a specific protein (integrase).
integrase: A protein that facilitates the insertion (integration) of one DNA molecule into another.
integration: A process in which one DNA molecule inserts into another.
integron: A region of DNA that contains an integration site, a gene encoding an integrase, and a promoter such that genes from other regions of DNA are inserted downstream from the promoter, assuring their capability to be expressed.
interference RNA: Small RNA molecules that hybridize to complementary RNA molecules, forming a hybrid that is then cleaved by an enzyme that recognizes double-strand RNA; used to selectively inactivate expression of particular genes.
interpretative breakpoint: See breakpoint.
isolate (noun): A pathogen sample taken from a patient.
isolate (verb): To separate a microbe or a particular type of molecule from other “contaminating” microbes or molecules.
hybridization: See nucleic acid hybridization.
latent infection: A situation in which a pathogen is present but undetectable by direct means.
lawn: A growth of bacterial cells that completely covers the surface of an agar plate.
longitudinal surveillance: Survey of antibiotic resistance conducted periodically, often annually, in the same patient population and geographic region to provide information about changes in the prevalence of resistance.
lysis: Break apart, commonly referred to host cells breaking apart during virus infection.
lysogeny: The process by which a bacterial virus integrates into the bacterial chromosome and remains quiescent.
macrophage: A type of mammalian cell that acts as a scavenger of foreign particles and microbes.
maximal concentration (Cmax): The highest level achieved by an antibiotic after administration.
messenger RNA (mRNA): A type of RNA that carries information from a gene in DNA to ribosomes where new protein is made using the nucleotide sequence in the mRNA to specify the number and order of amino acids in the new protein.
microbes: Cellular micro-organisms that include bacteria, yeasts, molds, and protozoa.
microbiome: The set of microbes carried by a multicellular host.
Minimal Bactericidal Concentration (MBC): The antibiotic concentration that causes a 99.9% decrease in microbial survival in a specified time, usually 18 hours for rapidly growing bacteria.
Minimal Inhibitory Concentration (MIC): Lowest concentration of an antibiotic that blocks the growth of a standard microbial inoculum, usually between 104 and 105 cells in the case of bacteria.
MRSA: Methicillin-resistant Staphylococcus aureus; a common commensal skin bacterium that can cause serious infections; commonly found on skin and inside the nose.
Multi-Drug Resistant (MDR): A microbe or virus resistant to more than one antibiotic; in the case of M. tuberculosis, MDR refers to bacteria resistant to isoniazid and rifampicin.
mutant: An organism or virus that has undergone a change in its genetic material (DNA or RNA) that causes the organism or virus to differ from the parental population (not a recombinant).
Mutant Prevention Concentration (MPC): Minimal concentration that blocks the growth of the least susceptible, next-step resistant mutant subpopulation; with bacteria MPC is approximated by the concentration that prevents colony formation when more than 1010 bacteria are applied to drug-containing agar.
mutant selection window: (See mutant selection window hypothesis).
mutant selection window hypothesis: The proposition that antibiotic-resistant microbes and viruses are selectively enriched and selectively amplified when antibiotic concentrations fall in a specific range (mutant selection window); the lower boundary of the range is approximated by MIC and the upper boundary by MPC.
mutation: A change in the genetic material (DNA or RNA) of an organism or virus; mutations are commonly insertions, substitutions, and deletions of nucleotides.
narrow-spectrum antibiotic: Having activity against only a few species.
neuraminidase: An enzyme on the surface of influenza virus that removes sugar groups from proteins and lipids; a component of influenza virus.
nonadherence to therapy: Failure of a patient to comply with a therapeutic regimen.
nucleic acid hybridization: A process in which two single-stranded nucleic acids from different sources form a double-stranded molecule due to complementary base pairing.
nucleoside analogues: A nucleoside similar to A, T, G, C, or U that can be incorporated into DNA or RNA but does not function like a natural nucleoside.
open reading frame (orf): A region of DNA or RNA that can encode a protein; a region of nucleotide sequence generally devoid of stop codons.
opportunistic infection: Growth of a microbe that normally does not occur with a healthy host due to action of host immune system; common examples are fungal infections of immunocompromised individuals.
pandemic: A disease outbreak that spreads to multiple countries.
pasteurization: Heating a liquid, such as milk, to slow spoilage; in practice, the heating eliminates 99.999% of the viable microorganisms.
pathogenicity island: A region of DNA in a microbial chromosome that 1) contains genes that contribute to pathogenicity and 2) is thought to have moved into the microbe as a block from another organism.
peroxide: A small oxygen-containing molecule of the form H2O2 (hydrogen peroxide); considered to be a reactive oxygen species and the precursor of hydroxyl radical.
persister: A member of a microbial population not killed by an antimicrobial but remains fully susceptible.
petri dish: A covered glass or plastic dish in which the lid is slightly larger than the dish, allowing the lid to cover the dish in a way that enables oxygen access to the interior of the dish while generally keeping contaminating microbes outside.
pharmacodynamics: The effect of an antibiotic treatment on a microbe.
pharmacokinetics: The relationship between drug concentration and time following drug administration.
plaque: A hole in a lawn of bacteria created by infection of bacterial cells by a virus.
plasmid: An autonomous DNA molecule residing in a microbial cell.
Polymerase Chain Reaction (PCR): A process by which a region of DNA is selectively amplified through repeated replication of the region by DNA polymerase.
post-antibiotic effect: Residual antibiotic action occurring after antibiotic concentration drops below toxic levels.
prevalence of resistance: The number of pathogen isolates having MIC greater than the interpretive breakpoint divided by the total number of isolates tested.
primer: A short nucleic acid used to initiate DNA replication at a specific location on a template nucleic acid.
probe: Generally a short nucleic acid used to detect the presence of a complementary nucleic acid in a patient sample.
promoter: A region of DNA, often upstream from a gene, at which RNA polymerase binds and begins transcription of the gene.
protein: Chain-like molecule composed of amino acids.
protein binding: Interaction of an antibiotic with serum or tissue; thought to reduce the effective concentration of antibiotics.
protein synthesis: The intracellular process of making new proteins; also called translation.
protozoan: A type of unicellular eukaryotic organism lacking a chloroplast or cell wall; examples are parasites that cause malaria and sleeping sickness.
quorum sensing: A process occurring in bacterial cultures in which small molecules released by one bacterium bind to another bacterial cell and cause a response in the second cell; the process is sensitive to cell density and therefore acts as a way for members of bacterial populations to sense when many members are present.
rational drug design: A process employed by the pharmaceutical industry in which the atomic structure of potential drugs and their biological targets are used to formulate new molecules likely to be highly active.
reassortment: The process occurring during influenza virus replication in which the eight viral RNA segments used to form mature virus particles are selected from a pool such that progeny viruses arising from an infection of a cell by two or more viruses contain a mixture of segments arising from the parental viruses.
recombination: Exchange of portions of DNA between two DNA molecules through a breakage and rejoining process.
relapse: Recurrence of disease following completion of treatment; generally associated with failure to remove the pathogen.
resistance mutations: Changes in the nucleotide sequence of DNA (RNA with same viruses) that enable an organism or virus to grow or at least survive treatment with an antibiotic at concentrations that inhibit growth or kill the parental organism or virus.
reverse transcription: The process of making a DNA molecule using RNA as a template.
ribosomal RNA (rRNA): A type of RNA that forms an integral part of ribosome structure.
ribosomes: Large intracellular structures composed of several ribosomal RNA molecules and many different ribosomal proteins; ribosomes serve as the intracellular sites where new proteins are made.
RNA: Ribonucleic acid; a long, thin chain-like molecule (nucleic acid) found in several varieties that have distinct functions.
RNA virus: A virus that uses RNA as its genetic material.
seasonal influenza: A respiratory disease caused by influenza virus that occurs each year during the winter and spring months.
serotype: A group of closely related microorganisms distinguished by a characteristic set of antigens, often thought of as a subspecies; also called a serovar.
site-specific recombination: DNA strand exchange taking place between segments possessing only a limited degree of nucleotide sequence homology; breaking and rejoining DNA at a specific location.
spore: A dormant body formed by certain bacteria, fungi, or other microbes that enables survival in adverse environmental conditions.
sputum: Material coughed from the respiratory tract, including saliva, mucus, and foreign material.
subpopulation: A minor subset of a heterogeneous population of microbes.
surveillance: The act of carefully watching; performing surveys to assess the prevalence and changes in prevalence of antibiotic resistance.
syncytium: A multinucleate mass of cytoplasm not separated into individual cells; created by infection with certain types of viruses.
template strand: The strand of DNA or RNA that serves as the source of nucleotide sequence information for formation of a second, complementary strand.
toxin-antitoxin module: A two-gene operon in which one gene encodes a poison and the other a protein that neutralizes the poison.
transduction: The process by which a virus moves genes from one cell to another.
transfer RNA (tRNA): A form of small RNA (generally shorter than 100 nucleotides) that serves as an adapter to order amino acids on ribosomes for incorporation into protein.
transformation: Change of form; with respect to bacteria, transformation refers to acquisition of a plasmid or other foreign DNA; with respect to animal cells, transformation refers to a normal cell becoming a tumor cell.
transposition: The process by which a transposon moves from one position in DNA to another. (Movement of many transposons is accompanied by making a copy of the transposon that moves.)
transposon: A segment of DNA capable of independently moving to a new position within the same or another DNA molecule.
vaccine: A biological preparation, often molecules characteristic of a pathogen or an attenuated pathogen, that enhances immunity to a specific disease by stimulating the immune system to recognize and destroy the pathogen when subsequently encountered.
viral receptors: Macromolecules, usually proteins or complex sugars, located on the surface of cells that enable attachment of virus particles.
virus: An infectious agent containing genetic material as either DNA or RNA surrounded by a protective protein coat; not capable of replication outside a living cell; generally submicroscopic.