BSCI 424 — PATHOGENIC MICROBIOLOGY

Basic Definitions

Achlorhydria (achlorhydric): no stomach acid; condition may be physiological or pharmacological (e.g., omeprazole (Prilosec^(R)) or other antisecretory proton-pump blocking drugs prescribed commonly for gastric ulcers)

Acute: course of a disease that is of sudden onset, marked intensity (relatively severe) and short duration (see chronic)

Adenosine triphosphate (ATP): a nucleotide that serves as the main energy source for metabolic reactions

Adherence (attachment): close association of bacterial cells and host cells generally characterized by receptors and target sites

Adhesin: structure or macromolecule located on the surface of a cell or extracellularly that facilitates the adherence of a cell to a surface or to another cell; site of attachment is often a specific receptor, but the adherence may also be nonspecific; host cell receptors are often sugar moieties (see lectin)

Alveolus (singular): air sac in lung; Alveoli: (plural of alveolus)

Amphiphilic: description of a molecule that has both a hydrophilic region and a hydrophobic region (e.g., lipopolysaccharide)

Anabolism (anabolic): energy-consuming metabolic process of combining smaller molecules into larger molecules that is driven by ATP (see also catabolism)

Anaerobe: an organism normally growing only in the absence of oxygen

Antibiotic: Substance produced by a microorganism or a similar product produced wholly (synthetic) or partially (semi-synthetic) by chemical synthesis and in low concentrations inhibits the growth of or kills microorganisms

Arthropod: member of phylum Arthropoda, including insects, arachnids, and crustaceans

Suffix "-ase": generally indicates an enzyme

Attachment: see adherence

Autolysin: autolytic enzyme important in enzymatically catabolizing peptidoglycan in pre-existing cell walls so that new cell wall could be "laid down" during bacterial cell division; also important component in cell lysis and resulting cell death during beta-lactam antibiotic inhibition of cell wall synthesis

Bacillary dysentery = dysentery caused by bacterial infection with invasion of host cells/tissues and/or production of exotoxins

Bacillus: any rod-shaped bacterial cell; bacilli (plural) (see also coccus; spirillum)

Bacteremia: presence of bacterial cells in the bloodstream

Benign: referring to a non-life or non-health threatening condition = commensalism

Beta-lactam: a class of antibiotics characterized by a beta-lactam ring structure (e.g., penicillins, cephalosporins)

Beta-lactamase: bacterial enzyme that degrades beta-lactam antibiotics by breaking beta-lactam ring

Benign: referring to a non-life or non-health threating condition; commensalism between host and parasite

b.i.d.: Twice daily (Latin, bis in die) (see also q.d.; q.i.d.; t.i.d.)

Biofilm: an adherent layer of bacteria and/or other microorganisms on a solid surface bound together in a bacterially-derived polysaccharide matrix that is protective for the organisms; generally occuring at a liquid/solid interface and often developing into a complex ecological community (e.g., dental plaque bound together by dextrans)

Catabolism (catabolic): energy-releasing metabolic process of breaking complex compounds into simpler ones (see also anabolism)

Catalase: an enzyme that catalyzes the breakdown of hydrogen peroxide to oxygen and water

  2 H₂O₂ à O₂ + 2 H₂O

Cecum (caecum): a large, "blind" pouch at the beginning of the large intestine extending from the terminal ileum to the colon, just posterior to the ileocecal junction

Cellulitis: inflammation of connective tissue underlying the skin

Chemoprophylaxis: use of a chemotherapeutic agent to prevent a specific disease

Chemotaxin (chemotaxigen): chemotactic factor

Chemotaxis: movement along a chemical concentration gradient; migration of granulocytes and macrophages toward higher concentrations of chemotaxins during the inflammatory response

Chemotherapy: the treatment of a disease with chemical agents or drugs; chemicals or drugs that affect a pathogenic microorganism negatively without harm to the host

Chronic: course of a disease persisting over a long period of time (see acute)

Class: taxonomic classification below phylum (or subphylum) and above order

Coccus: (singular): spherical-shaped cell; cocci (plural) (see also bacillus, spirillum)

Coliform bacteria (coliforms): any fermentative (specifically lactose-fermenting) Gram-negative anaerobic enteric bacilli (E. coli-like)

Colitis: inflammation of the colon

Colon: the major portion of the large intestine extending from the cecum to the rectum; ascending, transverse, descending, and sigmoid portions

Colonization: the successful occupation of a new habitat by a species not normally found in this niche

Commensalism: a relationship between two species (commensals) in which one is benefited and the other is not affected, neither negatively nor positively

Competition: simultaneous demand by two or more organisms or species for a necessary, common resource or physical space (niche) that is in limited or potentially limited supply, resulting in a struggle for survival

Conjugation: "bacterial sex;" the exchange of genetic material from one bacterial cell (donor) to another (recipient) by the close association of the two cells and the passage of the bacterial chromosome or plasmid through the F pilus

Cytokines: soluble molecules produced by cells that serve as mediators of intracellular reactions and biological response modifiers (e.g., lymphokines)

Degradative enzyme: class of protein capable of catalytic catabolic reactions

Disseminated intravascular coagulation (DIC): disorder characterized by a reduction in the elements involved in blood coagulation due to their utilization in widespread blood clotting within the vessels; late stages marked by profuse hemorrhaging

Diapedesis: passage of leukocytes and other plasma proteins out through blood vessel walls and into surrounding tissuesDigestive tract (alimentary canal): the "tube" that starts at the mouth and continues to the anus and is technically "outside" of the body proper consisting of the mouth, pharynx, esophagus, stomach, small intestine and large intestine

Duodenum: the short (approximately twelve fingerbreadths in length = about 10 inches) U-shaped upper (proximal) portion of the small intestine extending from the pyloric sphincter of the stomach to the jejunum, encompassing the superior, descending, transverse and ascending portions, in that order; hepatic ducts (from liver), pancreatic duct, and cystic duct (from gallbladder) join and enter into the intestine at the descending duodenum

Ecology: the study of the relationship between organisms and their environment

Edema: abnormal volume of fluid in intercellular tissue

Embolus (singular): a clot in a vessel obstructing blood flow; emboli (plural)

Empyema: pus accumulation in the lung(s) or other body cavity

Endemic: a disease or pathogen present or usually prevalent in a given population or geographic region at all times (see also epidemic)

Endocardium: membrane that lines interior of heart; innermost of two membranes that surround the heart

Endocarditis: inflammation of the endocardium (see also myocarditis)

Endocytosis: cellular uptake of material from the environment into an intracellular vesicle by invagination of the cell membrane; includes both phagocytosis and pinocytosis

Endogenous: originating from inside of host (see endogenous flora)

Endogenous flora: microbial flora occupying niche(s) that are in or on the body of the host

Endotoxin: complex bacterial toxin; Lipid A portion of lipopolysaccharide from Gram-negative cell walls; LPS is composed of Lipid A + Core Polysaccharide + O Antigen (a.k.a., O polysaccharide side chain) and is released upon lysis of the cell during infection ; Lipid A component is responsible for endotoxicity effects on the host; O side chain is the antigenic portion of the LPS molecule

Enteric (entero-): relating to the intestine (e.g., enteric infection)

Enterotoxin = an exotoxin with enteric activity, i.e., affects the intestinal tract

Eosinophils: 2-5% of total leukocytes; stain with eosin dye ; antiparasitic (e.g., intestinal worms)

Epidemic: a disease occuring suddenly in numbers far exceeding those attributable to endemic disease; occuring suddenly in numbers clearly in access of normal expectancy

Epidemiology: the study of factors influencing the occurence, transmission, distribution, prevention and control of disease in a defined population

Exotoxin: potent toxic substance formed and released extracellularly by species of certain bacteria; genetic control can be encoded either chromosomally, on a plasmid, or by a lysogenic bacteriophage (prophage) incorporated in either the chromosome or a plasmid

Facultative anaerobe: an anaerobe that can survive with or without oxygen

Fasciitis: inflammation of the fascia

Fermentation: the enzymatic breakdown (catabolism) of carbohydrates generally in the absence of oxygen

Fever (pyrogenicity): any elevation of the body temperature above the normal; functions to speed up immune reactions and to limit/slow bacterial growth and multiplication

Fibrin: insoluble protein that is main constiuent in blood clotting; formed by enzymatic cleavage of fibrinogen by thrombin

Fibrinolysin (staphylokinase; streptokinase; plasmin): enzyme capable of breaking down fibrin and thus dissolving blood clots

Fibroblast: connective tissue cell that that produces collagenous fibers and forms fibrous tissues

Fibronectin: two forms of adhesive glycoprotein found in host, important in cross-linking collagen in connective tissue (cell-to-cell binding), tissue repair and platelet aggregation

Fibrosis: formation of fibrous connective tissue; usually occurring with scar and granuloma formation

Fimbriae (plural): modern term for short, hair-like projections or appendages (organelles) on the outer surface of certain bacteria composed of protein subunits (pilin) extending outward from the surface that act as a virulence factor by promoting adherence; formerly known as pili; fimbria (singular)

Flagellum: whip-like bacterial locomotory (provide motility) organelles anchored in the cell membranes that are composed of helically-coiled protein subunits (flagellin); flagella (plural)

Flora: (Microbiology Definition); Microbiota: microorganisms present in or characteristic of a special location (niche) (Note: flora generically refers to plants; fauna generically refers to animals)

Glomerulonephritis: inflammation of the glomeruli in the kidney

Granulomatous: tending to form granulomas; usually referring to diseases or pathogenic microorganisms

Hematopoiesis: formation and development of blood cells

Hematopoietic (pluripotent; haemopoietic) stem cell: progenitor cell for all blood cells, including lymphoid (T- and B-lymphocytes), myeloid (mononuclear phagocytic system), monocytic, erythrocytic and megakaryoblastic (platelets) cell lines; primarily located in bone marrow

Hypotension: abnormally low blood pressure

Ileocecal junction: the site of transition from the terminal ileum of the small intestine to the cecum of the large intestine

Ileum: the lower (distal) portion of the small intestine extending from the jejunum to the ileocecal junction and encompassing approximately twelve feet in length (~3/5 of the length of the small intestine)

Infection: the i) colonization and/or invasion and ii) multiplication of pathogenic microrganisms in the host with or without the manifestation of disease

Infectious dose: the number of infecting organisms generally required to cause disease, in this case, via consumption of food

Inflammation (Inflammatory response): innate localized protective response of tissues to infection, disease or injury that functions to destroy, dilute or sequester the injurious agent and affected tissue; characterized physically by redness, heat, swelling, pain, impaired function and histologically by dilation and increased permeability of blood vessels, increased blood flow, diapedesis, chemotaxis and migration of plasma proteins and leukocytes to the focus of inflammation

Inoculum size: see dosage

Intestine: portion of the digestive tract between the pyloric sphincter of the stomach and the anus, composed of the small intestine and the large intestine

Invasins (invasive factors): structure or macromolecule that enables a pathogenic microorganism to enter and spread throughout the cells and/or tissues of the host body; specific recognition of receptor sites on target cells enhances pathogenic advantage

In vitro: literally meaning "in glass" and referring to assays performed in a test tube or another artificial laboratory environment

In vivo: literally meaning "in living" and referring to assays performed in a living animal

I.P. (IP): intraperitoneal (see also IV; PO)

Ischemia (ischemic): deficiency of oxygenation of a body part caused by obstruction in or constriction of blood vessel(s)

Suffix "-itis": generally indicates inflammation

I.V. (IV): intravenous (see also IP; PO)

Lamina propria: thin layer of fibrous connective tissue immediately beneath the surface epithelium of mucous membranes

Large intestine: the portion of the digestive tract that extends from the terminal ileum (ileocecal junction) of the small intestine to the anus (approximately 5 feet in length), composed of the cecum, colon and rectum and containing >10¹¹ bacteria per gram of feces with anaerobes 1000-fold more common than other microbes

Leukopenia: an abnormally low number (or an abnormal reduction in the number (-penia)) of leukocytes in the blood, specifically a count of 5000 or less per cubic millimeter

Lipopolysaccharide (LPS): amphiphilic molecule integrated in (hydrophobic end) and extending outward from (hydrophilic end) the outer membrane of Gram-negative bacterial cells; structurally composed of hydrophobic Lipid A (responsible for endotoxin activity) + Core polysaccharide + hydrophilic O-somatic antigen polysaccharide side chain; provides protection from environmental insults and acts as virulence factor

Lipoteichoic acid: amphiphilic molecule integrated in and extending outward from the cell wall (peptidoglycan layer) of Gram-positive bacterial cells; structurally composed of hydrophobic glycolipid and hydrophilic polyglycosyl-polyglycerophosphate; often serves as an antiphagocytic adhesin

Lumen: the space inside a tubular organ, e.g., a blood vessel or intestine

Lymph: clear extracellular fluid that is derived from tissue fluids, circulates in the lymphatic vessels and is filtered by the lymph nodes

Lymphangitis: inflammation of lymphatic vessel(s)

Lymphatic system (lymphatics): system of vessels, nodes, and masses of tissue , e.g., spleen, responsible for filtering lymphatic fluid from the tissues and recirculating it back to the venous system; also transports lipids and proteins to the circulatory system and returns fluid that leaks out of capillaries

Lymphatic tissue (lymphoid tissue): tissue consisting of lymphocytes enclosed in network of reticular and collagenous fibers

Lymphoid tissue: see lymphatic tissue

Lymph node: mass of lymphatic tissue located in lymphatic vessels and responsible for filtration of lymph

Lymphoblast: lymphoid tissue cell that is the immature precursor (progenitor) of a mature lymphocyte

Lymphocyte(s): mononuclear, nonphagocytic, immunologically competent leukocytes with agranular cytoplasm (agranulocyte) and large nucleus concentrated in blood, lymph and lymphoid tissue that are divided into two classes: B lymphocytes (B cells) and T lymphocytes (T cells); active in immunological responses in the body, including the production of lymphokines (cytokines) and antibodies

Lymphokine: extracellular soluble protein produced by T-lymphocytes that activate cell-mediated immunity and inflammation; type of cytokine

Lysogeny: the stable integration of DNA from a temperate bacteriophage (prophage) into the DNA of the host bacteria resulting in co-replication of the genome and acquisition of viral gene products and functions by the host

Macrophage: monocyte-derived large mononuclear phagocytic cell arising from hematopoietic stem cells in the bone marrow and mainly localized in the tissues; performs an array of immune response functions including nonspecific phagocytosis and pinocytosis, antigen presentation to T cells to initiate specific immune responses, secretion of lymphokines (cytokines)

Macrophage (a.k.a., mononuclear phagocyte): phagocytic cell (mononuclear leukocytes) active in tissues; characteristics di stinctive in different tissues; may become activated macrophages upon appropriate signals (e.g., cytokines like interferon-gamma) with increased efficiency and new functions

Malignant: referring to a disease tending to become progressively worse (morbidity = illness) and potentially result in death (mortality = death)

Mast cells: "tissue-based basophils;" contain histamine; function in allergic reactions, inflammation, other immune responses

M cells (microfold cells): specialized cells in the Peyer’s patches that sample the microenvironment and uptake foreign antigens for processing by underlying macrophages

Meningitis: inflammation of the meninges

Mesophile (mesophilic): liking moderate temperatures; optimal growth at 20^o to 45^oC

Metabolism: Sum total of all the chemical and physical processes within a living organism

Microaerophile (microaerophilic): an organism requiring oxygen for growth at a level below that found in air (normal air has an oxygen concentration of ~21%)

Microbial interactions: complex relationships among species; Neutral, Antagonistic, or Synergistic

Microbiota: microscopic flora

Mononuclear phagocyte system (monocyte-macrophage system): (formerly known as reticuloendothelial system): collective system of strongly phagocytic cells including: macrophages derived from monocytes; histiocytes; microglagia; mononuclear phagocytes (monocytes in blood; macrophages in tissues) and polymorphonuclear leukocytes (e.g., neutrophils, eosinophils)

Monocytes: Agranular (despite small lysosomes) mononuclear leukocytes circulate in blood for 1-2 days then migrate into tissue and become macrophages; capable of phagocytosis and have small granules (lysosomes) containing acid hydrolases and peroxidase

Morbidity: illness

Morphology: the study of form and structure of organisms (see also phenotype)

Mortality: death

Multiplication: the ability of a microorganism to reproduce and increase in numbers during an infection

Mutualism: mutually beneficial symbiotic relationship between two species

Myeloblast: see myeloid precursor cells

Myeloid precursor cells (a.k.a., myeloblast): give rise to mononuclear phagocyte system (monocyte-macrophage system formerly known as reticuloendothelial system)

Necrotizing: causing necrosis

Neuritis: inflammation of nerves or nerve cells (neurons)

Neuron: nerve cell

Neutropenia: an abnormal reduction in the number of neutrophils in the blood

Neutrophil (polymorphonuclear leukocyte) (PMN): granular leukocyte (granulocyte) with multilobed nucleus that is chemotactic, phagocytic, and adherent to immune complexes; primary phagocytic defense against bacterial cells (antibacterial and antifungal); main functions are rapid chemotaxis to and phagocytosis of invading microorganisms; appear first in response to inflammation and produce chemotaxins to attract more PMNs and other mononuclear phagocytes (monocytes; macrophages); present in circulation and can migrate into tissues (diapedesis) with a 2-3 day lifespan

Normal flora: (a.k.a., indigenous or resident flora or microbiota) those microbial flora typically occupying a particular niche; given diversity of environmental conditions, organisms tend to segregate; many normal flora perform important functions for the host, including: digestive and nutritional functions and competition with pathogenic microorganisms (see also Transient Flora)

Nosocomial (nosocomial infection): an infection acquired in the hospital that was not present in the host nor incubating prior to admission and generally occurring within 72 hours after admission

Nutrient Availabilty: the accessibility of a necessary resource, substance or compound providing nourishment to maintain life, i.e. capable of conversion to energy and structural building blocks

Ontogeny: Developmental history of an individual organism; "Ontogeny recapitulates phylogeny"

Osmotic pressure (p): expressed in units of atmospheres; reflects the concentration of solute in an aqueous solution

Petechiae (plural): round, purple lesions caused by intradermal or submucosal microvascular hemorrhaging, capillary leakage or microhemorrhage; petechia (singular)

Peyer’s patch: aggregations of lymphoid tissue concentrated in the ileum

pH: power of hydrogen; measurement of the amount of hydrogen ion in solution; logarithm of the reciprocal of the hydrogen ion concentration in an aqueous solution used to express its acidity or alkalinity (range from 0-14)

Phylogeny: Evolutionary history of a species or other taxonomic group

Physiology: the study of organic processes or functions of living organisms or parts of organisms

Pleomorphic: taking a variety of shapes and forms; multiple morphologies

Point-source outbreak: large numbers of people acquiring infection and disease from a common source and within a limited period of time (see also sporadic cases)

Polymorphonuclear leukocytes (a.k.a., PMNs; neutrophils, granulocytes; polymorphs; "morphs"): granular leukocytes with single multilobed nucleus; differentiated into classes on basis of dye uptake; constitute 50-70% of circulating leukocytes; 60-70% of all leukocytes are granulocytes and 90% of these are neutrophils; stain with neutral dyes (see also neutrophil)

Porin: major proteins in Gram-negative cell outer membranes grouped as dimers or trimers to form transmembrane channels that allow transport of certain molecules into the cells; "cellular pores"

Portal (route) of entry or exit: means by which an infectious agent enters the host; three portals of entry: i) inhalation, ii) ingestion, iii) direct penetration

Prevalence: number of cases of disease occurring within a population at any one given point in time (see also incidence)

Primary (azurophilic) granules (a.k.a., lysosomes): contain acid hydrolases, myeloperoxidase and lysozyme

Psychrophile (psychrophilic): liking cold temperatures; optimal growth at 15^o to 20^oC

Purpura: purple patches on skin due to microhemmorhaging in skin, mucous membranes or serosal surfaces

q.d.: Every day; Once per day (Latin, quaque die) (see also b.i.d; q.i.d.; t.i.d.)

q.i.d.: Four times per day (Latin, quater in die) (see also b.i.d; q.d.; t.i.d.)

Rectum: the short terminal (distal) portion of the large intestine extending from the terminal colon to the anus

Reticuloendothelial system: see mononuclear phagocyte system

Sebacious gland: holocrine gland in the skin that secretes sebum into hair follicles

Sebum: fatty secretion of the sebacious glands; thick greasy semifluid lubricating substance composed of fat and epithelial debris

Secondary granules: (specific) granules contain lactoferrin and lysozyme; oxygen-dependent (respiratory burst) and oxygen-independent (cationic proteins, lysozyme, lactoferin) killing

Spheroplast: osmotically-sensitive cell lacking rigidity of and structural containment supplied by cell wall

Spirillum: any helically-shaped (spiral) bacterial cell; spirilla(plural) (see also bacillus, coccus)

Sporadic cases: infections and disease occuring randomly throughout a population (see also point-source outbreak)

Stem cell: in developmental biology, a cell that proliferates indefinately and that, by differentiating into specialized cells, can serve as a continuous source of new tissue and blood cells (e.g., hematopoietic stem cells)

  Antibiotic synergism: when the effects of combined antibiotics are greater than the sum of the individual effects

  Bacterial synergism: when the effects of mixtures of bacteria are greater than the sum of their individual effects (e.g., in reference to pathogenicity)

Tenesmus: straining to defecate

Thermophile (thermophilic): a microorganism that grows at elevated temperatures

Thrombolytic: capable of lysing (dissolving) a thrombus

Thrombosis: formation, development or presence of a thrombus

Thrombus (singular): "clot" in a blood vessel; aggregation of blood factors, including platelets, fibrin, clotting factors, and other cellular elements attached to the inside wall of a blood vessel that often causes occlusion (blockage); Thrombi (plural)

t.i.d.: Three times daily (Latin, ter in die) (see also b.i.d; q.d.; q.i.d.)

Toxoid: a protein toxin that has been altered with formaldehyde to lose physiological toxicity while retaining antigenicity; useful in immunization and common method for early vaccine formulations

Transduction: the transfer and recombination of genetic material from one bacterial cell (during the viral lytic cycle) into the genome of another bacterial cell (lysogeny) by a bacteriophage

Transformation: the uptake and incorporation of foreign (donor) "naked" DNA from the environment into the genome of a recipient cell

Transient flora: microbial flora only temporarily associated with a particular niche (see also Normal Flora)

Transmission: the passage or transfer of a disease from one host to another

Transposon: transposable genetic element; DNA sequence capable of replicating and inserting new copy in different site in genome; carries genes for its own transpositon as well as for other functions (e.g., antibiotic resistance)

True pathogen: any microorganism capable of causing disease; an infecting agent (see also Opportunistic Pathogen)

Vector: carrier of an infectious agent; capable of transmitting infection from one host to another; especially the animal that transfers an infectious agent from one host to another, usually an arthropod

Virulence: a measure of pathogenicity; a measurement of the degree of disease producing ability of a microorganism as indicated by the severity of the disease produced; a measure of the dosage required to caused a specific degree of pathogenicity --- one general standard is the LD50

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