Our Glossary

Ames – A test used to determine the effects of a chemical on the rate of mutation in bacterial cells, and hence its likely potential for causing cancer in other organisms, including humans.

Devised by US biologist Bruce Ames, it is widely used in screening chemicals occuring in the environment for possible carcinogenic activity.

The chemical being tested is applied to plates inoculated with a special mutant strain of bacteria (usually Salmonella typhimurium) that require the amino acid histidine for growth. Cells that mutate back to the wild type are detected by the occurance of colonies able to synthesise their own histidine and therefore grow on the medium.

Antibiotic Resistance – The acquired ability of a microorganism to grow in the presence of an antibiotic to which the microorganism is usually sensitive.

Antimicrobial Agent – A chemcial that kills or inhibits the growth of microorganisms.

Antimicrobial Drug Resistance – The acquired ability of a microorganism to grow in the presence of an antimicrobial drug to which the microorganism is usually susceptible.

Antimicrobial Susceptibility Testing (AST) – A procedure used to determine which antibiotics a specific organism or group of organisms are susceptible to.

Pathogens isolated from clinical specimens are identified to confirm medical diagnoses and to guide antimicrobial therapy to ensure the correct antibiotics are used and avoid using antibiotics that the pathogen may be resistant to.

The standard procedure for assessing antimicrobial activity is the disc diffusion test. Agar is evenly inoculated with a suspension of pure culture onto the surface. Filter paper discs containing a specified dose of antimicrobial agent are placed onto the inoculated agar. After a specified incubation period, the diameters of the inhibition zones formed around each disc are measured. Inhibition zone diameters are then interpreted into susceptibility categories based on the zone size (Susceptible, Intermediate, Resistant) set by organisations such as EUCAST or CLSI.

Another procedure now being more commonly used is the MIC (minimum inhibitory concentration) method. The MIC procedure utilizes an antibiotic dilution assay in agar, within culture tubes or within micro titre plates. When using the MIC method within culture tubes or micro titre plates, serial dilutions of antibiotics are inoculated into the well or tubes alongside a standard inoculum of a test organism. Growth in the presence of each antibiotic concentration is measured using turbidity. Antibiotic susceptibility is stated as the highest dilution or lowest concentration of antibiotic that completely inhibits growth. When using the MIC method on agar, an inoculated diffusion strip containing an antibiotic concentration gradient is applied to the agar. When applied to the agar, the gradient transfers from the strip into the agar. After overnight incubation or longer, an elliptical zone of inhibition centered around the strip forms. The MIC value can be read at the point the ellipse edge intersects the MIC strip. The resulting MIC value can then be interpreted using standards such as EUCAST or CLSI.

Bacillus – Any rod-shaped bacterium.

Generally, bacilli are large, Gram-positive, spore-forming and have a tendency to form chains and produce a capsule. Some are motile bearing flagella.

Bacilli are ubiquitous in soil and air and many are responsible for food spoilage.

Bacteria – A diverse group of ubiquitous microorganisms all of which consist of only a single cell.

Bacteria can be characterized in a number of ways, for example their reaction with Gram’s stain or on the basis of their metabolic requirements (e.g. whether they require oxygen) or shape. A bacterial cell may be spherical (coccus), rodlike (bacillus), spiral (spirillum), comma shaped (vibrio), corkscrew-shaped (spirochaete), or filamentous. The majority of bacteria range in size from 0.5 to 5 um. Many are motile, bearing flagella. Some can produce endospores.

In general bacteria reproduce only asexually, by simple cell division, but a few groups undergo a form of sexual reproduction in the form of conjugation.

Bacteria are largely responsible for decay and decomposition of organic matter, creating by-products such as carbon, oxygen, nitrogen and sulphur when using organic matter as a fuel. A few bacteria obtain their energy by means of photosynthesis (such as cyanobacteria), some are saprotrophs and others are parasites, causing disease.

The symtoms of bacterial infections are produced by toxins released by the bacteria.

The number of viable microorganisms present on a surface/in a sample.

A colony forming unit, or CFU, is a unit commonly used to estimate the concentration of microorganisms in a test sample. The number of visible colonies (CFU) present on an agar plate can be multiplied by the dilution factor to provide a CFU/ml result.

Specialized type of media combining selective ingredients and chromogenic substrates to increase the reliability of bacterial/fungal identification. Each test organism has enzymes that act on the substrates to release chromogens, resulting in a distinct color change in the medium or colonies.

The Clinical and Laboratory Standards Institute (CLSI) is a non-profit US-based organization that supports the development of scientific and clinical standards and guidelines.

Coccus – Any spherical bacterium.

Cocci may occur singularly, in pairs, in groups, in cubical packets, in grapelike clusters or in chains.

Cocci are generally non-motile and do not form spores.

The most prominent pathogenic species are Staphylococci and Streptococci.

Conjugation – The transfer of genes from one prokaryotic cell to another by a mechanism involving cell-to-cell contact.

Conjugation is a form of sexual reproduction in bacteria. Two individual cells are united by a tube formed by outgrowths from one or both cells. Genetic material from one cell (designated the male) then passes through the tube to unite with genetic material in the other cell (designated female).

Bacterial conjugation is initiated and directed by sex factors located in bacterial plasmids.

Endospore – A differentiated cell formed within cells of certain Gram-positive bacteria that are extremely resistant to heat and other harmful conditions and agents.

Endopsore are the resting stage during the life cycle of some bacteria, formed in response to adverse conditions. The bacterial cell changes into a partially dehydrated core, enclosed in a multilayered protein coat. On return to favorable conditions the spore germinates and reverts back to the normal vegetative form of the organism and continues its life cycle.

Endospores can remian viable for long periods of time, potentially thousands of years.

Enteric bacteria – A large group of gram-negative, rod-shaped bacteria characterized by an aerobic metabolism and commonly found in the intestines of animals.

The European Committee on Antimicrobial Susceptibility Testing (EUCAST) deals with antimicrobial susceptibility breakpoints and MICs of antibiotics.

Fungi – A group of eukaryotic microorganisms which feed on organic matter.

Fungi can either exist as single cells or make up a multi-cellular body called mycelium. Mycelium consists of filaments known as hyphae. Most fungal cells are multi-nucleate and have cell walls composed of chitin.

Fungal cells obtain nutrients either through parasitic or saprophytic means as they do not contain chlorophyll to perform photosynthesis. The cells secrete extracellular enzymes that can breakdown complex organic matter, such as proteins or polysaccharides, into simple sugars, amino acid etc. The broken-down nutrients are then assimilated into the fungal cells as sources of energy. Most plants are dependent on specific fungi to enable them to uptake certain minerals and nutrients they require from the soil. Fungi which have this relationship with plants form a symbiotic relationship and grow around the plant roots, this is called mycorrhizae (fungus roots).

Some fungi form spores as a results of sexual reproduction. Sexual spores of fungi are typically resistant to freezing, heating, drying out and some chemicals. However, fungal spores are not as resistant to heat as bacterial endospores.

Fungi exist primarily in damp situations on land.

Gram Stain – A differential staining technique in which cells either stain pink (gram-negative) or purple (gram-positive) depending upon their structural type.

During a gram stain, a bacterial sample is smeared on a microscope slide and allowed to dry. The slide is then stained with a violet dye, treated with acetone-alcohol (a decoloriser) and finally counter-stained with a red dye.

Gram-positive bacteria retain the first violet dye as they have a thick layer of peptidoglycan in their cell walls creating cells which appear violet.

In gram-negative bacteria, the acetone-alcohol washes out the violet dye and the counter-stain is taken up creating cells which appear red. The cell walls of gram-negative bacteria have an outer layer of lipoprotein overlaying a thin layer of peptidoglycan.

Example process:

• slide stained with crystal violet (1 min),
• rinsed with water,
• stained with iodine (1 min),
• rinsed with water,
• destained with acetyl-choline,
• rinsed with water,
• counterstained with safranin (1 min)

Samples such as water are often tested for microorganisms by passing the sample through a membrane filter of known pore size (e.g. 0.45 µm) and incubating the filter on a suitable medium.

The Minimum Inhibitory Concentration (MIC) of an antimicrobial agent is the lowest concentration of that agent that will prevent or ‘inhibit’ microbiological growth.

Microbiology – The scientific study of microorganisms (eg Bacteria, Viruses and Fungi).

Originally the study of microbiology was directed towards the effects of microorganisms (eg how they cause disease and decay). However during the 20th century, the emphasis shifted to their physiology, biochemistry and genetics. Microbes are now recognized as important vehicles for the study of biochemical and genetic processes common to all living organisms, and their rapid growth enables their laboratory culture in large numbers for studies in genetics.

Microorganism – A microscopic organism consisting of a single cell that can only be observed with the aid of a microscope.

Morphology is the visual appearance of a microorganism, including its size, shape and the presence/absence of flagella.

OPKA – Opsonophagocytic Killing Assay.

An assay used to measure the functional capacity of vaccine-candidate raised antibodies. The assay aids in selecting promising vaccines by demonstrating whether the vaccine induced antibodies drive efficient complement deposition and subsequent opsonophagocytic killing.

OPKA makes it possible to reproducibly estimate the phagocytic titre of sera from vaccinated and un-vaccinated individuals.

The assay is used commonly to assess pneumococcal vaccine immunogenicity.

Pathogen – Any disease causing microorganism. Pathogens include bacteria, fungi and protozoans.

Penicillins – Antibiotics derived from the mould Penicillium notatum.

Specifically know as Penicillin G and belongs to a class of similar substances called penicillins. They are all active against a wide variety of bacteria, producing their effects by disrupting synthesis of the bacterial cell wall, and are used to treat a variety of infections caused by bacteria.

Plasmid – An extra chromosonal genetic element that is not essential for growth present within some bacterial cells.

A plasmid is made up of DNA that can exist ad replicate independently of the chromosome. Plasmids provide genetic instructions for certain cell activities (eg antibiotic resistance). They can be transferred from cell to cell in a bacterial colony using sex factors to commence conjugation.

Plasmids are widely used as vectors to produce recombinant DNA for gene cloning.

SBA – Serum Bactericidal Antibody Assay.

SBA is used as a measure of antibody function in conjunction with complement to kill bacteria.

The assay can give information on whether any particular serum sample has a level (titre) of bacteriocidal antibodies sufficient to reach a protective threshold. SBA assays can also provide a percentage seropositivity (%SP) of subjects suppasing the protective threshold.

Spirillum – Any rigid spiral-shaped bacerium.

Generaly, spirilla are Gram-negative, aerobic and highly motile using a single or multiple flagella.

Spirilla occur in soil and water and feed on organic matter.

Spirochaete – Any non-rigid corkscrew-shaped bacterium.

Spirochaete move by means of flexions of the cell, produced by a series of rotary axial fibrils underlying the cell’s outer sheath.

Most spirochaetes are Gram-negative, anaerobic and feed on dead organic matter. They are particularly common in sewage-polluted waters.

Spirochaetes can cause disease in humans and animals. Treponema is the agent of syphilis.

Radial Immunodiffusion is a technique used extensively for the quantitative estimation of antigens.

Antibody of known specificity is distributed evenly in an agar gel and a sample containing the antigen of interest is placed in a well within the gel. Antigen then diffuses radially from the well and a precipitin ring forms at the point of antibody-antigen equilibrium. Antigen concentrations are determined by measuring the diameter of precipitin rings and extrapolating using standard curves.

Sterility tests are commonly carried out in pharmaceutical and medical device laboratories to assess the effectiveness of a sterilization process. The most common methods are direct immersion, membrane filtration and product flush.

Avaccine is a biological preparation that improves an individual’s immunity to a particular disease. Vaccines usually contain toxins, surface proteins or weakened/killed forms of microorganisms to stimulate the body’s immune system. If the individual comes into contact with that microorganism again, the body’s immune system will ‘remember’ it and destroy it more efficiently.

Vibrio – Any comma-shaped bacterium.

Generally, vibrios are Gram-negative, aerobic and motile.

Vibrios are widely distributed in soil and water and while some feed on dead organic matter, some are parasitic such as Vibrio cholerae, the causal agent of cholera.

Virus – A particle which is capable of independent metabolism and reproduction within a living cell. Outside its host cell, a virus is completely inert.

A mature virus (a viron) ranges in size from 20 to 600 nm in diameter. It consists of a core of nucleic acid (DNA or RNA) surrounded by a protein coat (Capsid). Some bear an outer envelope consisting of proteins and lipids (enveloped viruses).

Inside its host cell the virus initiates the synthesis of viral proteins and undergoes replication. The new virons are released once the host cell disintegrates.

Viruses are parasites of animals, plants and some bacteria (bacteriophages).

Antiviral drugs are effective against certain viral diseases and vaccines provide protection against others.

Common animal viruses include: HIV (AIDS), Influenza (Flu) and Herpes simplex (Herpes).