Dr. Abdelraouf A. Elmanama

Ph.D Microbiology

Abscess: pocket of pus; pus-filled lesion

Acidoduric: an organism capable of surviving under acidic conditions, e.g. Streptococcus mutans

Acidogenic: an organism capable of generating localized acidic conditions, e.g., Streptococcus mutans

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)

Actin: i) protein involved in smooth muscle contraction and relaxation; ii) protein that forms microfilaments at the cellular level that enable the movement of certain intracellular materials

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

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.

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.

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

Attachment: 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) 

Bacteremia: presence of bacterial cells in the bloodstream

Bactericidal: able to kill bacteria; e.g., serum has innate ability to kill many microorganisms

Bacteriophage (phage): a virus whose host is a bacterium; infects host bacterial cell resulting in either replication and transmissible lysis (lytic) or lysogeny (lysogenic prophage)

 Temperate phage: avirulent bacteriophage that rarely causes lysis of host cells; capable of entering into lysogeny

 Lytic phage: a bacteriophage that produces infection and lysis of susceptible bacterial cells

Bacteriostatic: inhibiting the growth of bacteria

Basophils: < 0.2% of leukocytes; stain with basic dyes; contain histamine; function in allergic reactions, inflammation, and other host immune responses; "circulating mast cells;" can also migrate into tissues

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)

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)

Bulla (singular): fluid-filled blister or vesicle; bullae (plural)

Capnophile (capnophilic): an organism requiring carbon dioxide at a level exceeding that of air (concentration of carbon dioxide in normal air is ~0.033%) for growth or for enhancement of growth

Capsule: Polysaccharide or protein layer surrounding the surface of some bacterial cells and is a major virulence factor that is poorly antigenic and antiphagocytic and functions in adherence and as a protective barrier.

Carbuncle: a coalescence or cluster of furuncles (boils);

Carrier (carrier state): a symptomless (asymptomatic) individual who is host to a pathogenic microorganism and who has the potential to pass (transmit) the pathogen to others

Carrier state: the condition of being a carrier; carriage may be transient or (semi-) permanent

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

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

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.

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

Coccus: (singular): spherical-shaped cell; cocci (plural) 

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)

Debridement: referring to the removal of dead, damaged, or infected tissue to improve the healing potential of the remaining healthy tissue.

Defensin(s): Small antimicrobial cationic peptides that are widely distributed and disrupt membrane integrity; Abundant in neutrophilic granules

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

Disease: an abnormal condition of body function(s) or structure that is considered to be harmful to the affected individual (host); any deviation from or interruption of the normal structure or function of any part, organ, or system of the body; dependent upon the dosage and virulence of the organism/agent and varies inversely with the resistance of the host

Dosage (inoculum size): the number of pathogenic microorganisms entering the host

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

Dysentery = inflammation of intestines (especially the colon (colitis) of the large intestine) with accompanying severe abdominal cramps, tenesmus, and frequent, low-volume stools containing blood, mucus, and fecal leukocytes (PMN's)

Dysuria: painful or difficult urination

Ecological relationship (ecological community; ecosystem): the relationship between organisms and their environment (including other organisms)

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

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

Endocarditis: inflammation of the endocardium

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

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

Erythrocyte: red blood cell

Etiology: the cause or origen of a disease; the study of the cause(s) of disease

Exogenous:originating external to host

Exogenous flora: microbial flora normally existing externally to the body of the host

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

Exudate: fluid, cells, or cellular debris that has escaped from blood vessels and has been deposited on or in tissues

Facultative: ability to adapt and live under various conditions.

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

Family: taxonomic level below order and above genus

Fascia: sheet of fibrous tissue below the skin or surrounding muscles or groups of muscle fibers (see fasciitis)

Fasciitis: inflammation of the fascia

Fastidious: complex nutritional or cultural requirements, making isolation and culture of a fastidious organism more difficult

Fauna: ecological term that generically refers to animals; flora generically refers to plants

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)

Follicle: small cavity or sac in organ or tissue; e.g., hair follicle or ovarian follicle

Folliculits: infection and inflammation of follicle(s)

Fomite: inanimate object capable of transmitting infectious organisms to a host, e.g., soiled bed linens, diapers, tissues and handkerchiefs, hospital respiratory equipment, dishrags, etc.

Furuncle: boil; a painful nodule in the skin caused by inflammatory sequestration of staphylococci and core formation

Furunculosis: perisistent sequential occurence of furuncles over a period of weeks or months

Genotype: the genetic make-up of an organism that combined with environmental factors contributes to the phenotype of the organism

Genus: taxonomic level below family and above species

Glomerulus (singular): spherical cluster of capillaries in the kidney where plasma is filtered ; glomeruli (plural)

Glomerulonephritis: inflammation of the glomeruli in the kidney

Glycocalyx: alternative term for capsule or slime layer

Granules: reservoirs for hydrolytic and digestive enzymes in certain types of phagocytic cells; delivered to phagosomes to form phagolysosomes to digest phagocytosed (a.k.a., phagocytized) foreign material; appearance under microscopy makes cells looks "granulated" (see primary granules and secondary granules)

Granulocyte (polymorphonuclear leukocyte): leukocyte with intracellular granules and multilobed nucleus

Granuloma: small growths of nodular granulation tissue formed at sites of chronic inflammation that are usually composed of epithelioid cells, lymphocytes, multinucleated giant cells, eosinophils, plasma cells that are "walled off" by an area of fibrosis

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

Hemolysin: bacterial protein exotoxin capable of hemolysis

Hemolysis: the lysis of red blood cells (erythrocytes); either in vivo in the host or in vitro on blood agar artificial medium

      Beta-hemolysis: complete hemolysis; clear zone around colonies on blood agar medium
      Alpha-hemolysis: partial hemolysis, usually with greening of the medium due to the reduction of  hemoglobin in the erythrocytes to methemoglobin
      Gamma hemolysis: no hemolysis

Hepatocyte: liver cell

Host: an organism (animal or plant) that harbors or provides nutrition for another organism (parasite; pathogen)

Host immune system: the cells and tissues involved in recognizing and attacking foreign substances in the body

Hyaluronic acid: a mucopolysaccharide that lubricates tissues and inhibits dissemination of invading microorganisms

Hyaluronidase: enzyme that breaks down hyaluronic acid; normally found in the spleen and the testicles and produced by species of Streptococcus and Staphylococcus

Hydrophilic: compatible with water; "water-loving"

Hydrophobic: incompatible with water; "water-hating"

Hypochlorhydria (hyperchlorhydric): abnormally low production of gastric acids

Hypoglycemia: abnormally low glucose levels

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

Impetigo: Pyoderma with yellowish weeping vesicular lesions that crust over when the pustule erupts historically seen on the face around the nose and mouth or on the limbs in children

Incidence: rate of occurrence of an event; number of new cases of disease occuring over a specified period of time; may be expressed per a known population size .

Incubation period: latent period between the time that infecting organisms enter the host and onset of signs and symptoms of disease

Independence: an ecological relationship in which an organism is living free from the influence, guidance, or control by another organism

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 (

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

"-itis" Suffix : generally indicates inflammation

I.V. (IV): intravenous

Jejunum: the middle portion portion of the small intestine, approximately eight feet in length (~2/5 of the length of the small intestine), extending from the duodenum to the ileum

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

Latent period (Latency): see incubation period

Lectin: adhesin specific for polysaccharide target receptor (sugar residues)

Lethal Dose 50% (LD50): the number of microorganisms required to cause lethality (mortality) in 50% of the test host

Lesion: pathological or traumatic discontinuity of tissue or loss of function

Leukocyte: white blood cell

Leukocytosis: an abnormally large number (or an abnormal increase in the number (-cytosis)) of leukocytes in the blood, as during hemorrhage, infection, inflammation, or fever, specifically a count of 12,000 or more per cubic millimeter

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 : tissue consisting of lymphocytes enclosed in network of reticular and collagenous fibers

Lymphoid tissue:  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

Macrolide: class of antibiotics produced by species of Streptomyces and containing a large oxygenated lactone ring (e.g., erythromycin, azithromycin)

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

Meninges: three membranes covering the brain and spinal cord; Dura mater (outermost), pia mater (middle), and arachnoid (innermost)

Meningitis: inflammation of the meninges

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

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 20.9%)

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

Microbiota: 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.

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)

Natural antibodies: Undifferentiated serum globulins

Necrosis: localized death of cells, tissue, or organ in response to disease or injury; sum of morphological changes indicative of cell death and caused by the progressive degradative action of cellular components, metabolic byproducts, enzymes and/or toxins

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

Niche (ecological niche): unique environmental position occupied by a particular species, perceived in terms of actual physical space occupied and function that it performs within the ecological community (ecosystem)

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

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"

Order: taxonomic classification below class and above family

Opportunist (opportunistic pathogen): an organism that is pathogenic only under certain conditions, but nonpathogenic under normal conditions; a usually harmless microorganism that becomes pathogenic under favorable conditions; often a member of the normal microbial flora

Opportunistic infection: infection caused by a normally harmless microorganism (opportunist) when certain predisposing conditions (disease or conditions that increase host susceptibility) exist

Organ necrosis: see necrosis

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

Oxidase: oxidoreductase that catalyzes oxidation of substrate with O2

Pandemic: a widespread epidemic distributed or occuring widely throughout a region, country, continent, or globally

Parasite: an organism benefiting from living in or on another organism

Parasitism: a relationship between two species in which one benefits (parasite) from the other (host); usually involves some detriment to the host

Pathogenicity: the quality of producing or the ability to produce pathologic changes or disease

Pathogen: an infecting agent (microorganism) capable of causing disease

  Opportunistic pathogen: a usually harmless microorganism that becomes pathogenic under favorable conditions
  True pathogen: any microorganism capable of causing disease; an infecting agent

Peritoneum: membrane lining the abdominopelvic wall

Peritonitis: inflammation of the peritoneum

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)

Phage:  bacteriophage

Phagocyte: specialized cell capable of internalizing and usually destroying foreign particulates or microorganisms

Phagocytosis: the process of engulfing and digesting extracellular foreign materials

Phagocytosis inhibitors: mechanisms enabling an invading microorganism to resist being engulfed, ingested, and or lysed by phagocytes/ phagolysosomes; patients with a defective/compromised monocyte-macrophage system (formerly, RES, reticuloendothelial system) are particularly susceptible to infection

Phenotype: the appearance and characteristics of an organism that derive from the interaction of genotype (genetic make-up) and environment

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

Pili (plural): former term for fimbriae (still used as alternative term); term more properly applied to those organelles (F-pilus) responsible for bacterial conjugation (transfer of nucleic acids between closely related strains or species = "bacterial sex"); F pilus (sex pili) are hollow organelles that allow for the transfer of portions of a bacterial chromosome from a donor cell to a recipient cell (conjugation); pilus (singular)

Plasma: fluid portion of blood or lymph containing suspended particulate components.

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

Pleura: serous membrane investing the lungs and lining thoracic cavity

  Visceral pleura: pleura surrounding lobes of lungs and lining the lung tissues
  Parietal pleura: pleura lining walls of thorax
  Pleurisy: chest pain deriving from inflammation of pleura

Pneumonia: inflammation of the lungs with consolidation as the lung becomes firm (solid) as alveoli are filled with exudate

P.O.: per oral; by mouth

Point-source outbreak: large numbers of people acquiring infection and disease from a common source and within a limited period of time

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

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

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

Prodrome (prodromal period): (period of) precursor symptom(s) indicative of the imminent onset of morbidity or disease

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

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

Purulent: consisting of or containing pus

Pus: viscous yellowish fluid product of inflammatory response that contains dead leukocytes in a thin liquid (liquor puris)

Pyoderma: any purulent skin disease

Pyogenic: pus-producing; "pyo-" = pus; "-genic" = generation of

Pyrogenic: causing fever; "pyro-" = fire

Pyuria: pus in the urine

q.d.: Every day; Once per day (Latin, quaque die)

q.i.d.: Four times per day (Latin, quater in die)

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

Reticuloendothelial system: see mononuclear phagocyte system

Saprophyte: an organism (bacteria, fungi) that utilizes decaying material as a primary nutritional source

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

Secretory IgA (sIgA): mucosal IgA; antigen-binding site attaches to target bacteria and Fc portion binds mucin, trapping/clearing bacteria

Septicemia (sepsis): systemic disease associated with persistent presence of bacterial cells, bacterial toxins or other bacterial products in the bloodstream

Serum: fluid portion of blood minus cells and clotting factors; inherently fatal to many microorganisms (serum killing; serum sensitivity).

Sequela (singular): a follow-on (sequel) to a disease; Sequelae: (plural of sequela)

Siderophore: extracellular iron-chelating compounds ("sidero-" = iron; "-phore" = a carrier)

Signs (Clinical): Objective evidence of a disease as observed by the physician

Slime layer: a diffuse or loosely-fitting capsule; also known as glycocalyx

Small intestine: the portion of the digestive tract between the stomach and the ileocecal junction at the beginning of the large intestine; composed of the duodenum, jejunum, and ileum; approximately twenty feet in length

Species: taxonomic level below genus and above subspecies

  sp. = abbreviation for single species
  spp. = plural abbreviation of species; multiple species
  (Note that sp. and spp. are not underlined or italicized)

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

Spirillum: any helically-shaped (spiral) bacterial cell; spirilla(plural)

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)

Streptokinase (fibrinolysin): extracellular enzyme of streptococci that catalyzes the conversion of plasminogen to plasmin; used clinically to dissolve blood clots (thrombi)

Subacute: course of a disease that falls somewhere between acute and chronic

Subspecies: taxonomic level below species (ssp. = abbreviation for subspecies)

Suppurative: producing pus

Symbiosis: a relationship in which two dissimilar organisms (symbiotes, symbionts) live in close association with one another

Symptoms: Subjective evidence of disease as reported by the patient (host)

  Note, therefore, that animals do not have symptoms, only signs, since they cannot talk to the veterinarian

Syndrome: Collection of signs and symptoms characterizing a particular morbidity

Synergism: combined effects greater than sum of individual effects

  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)

Taxonomy: the system of description, naming and classification of organisms into orderly categories based upon organismal interrelationships

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) (

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.

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

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