PhylumClassOrderFamilyGenusSpecies/Subspecies

Terms

Contents
Adherence [under revision]
Anaerobic cultivation
Bacteriophages
Biofilm
Colony Forming Unit (CFU)
Counting bacteria
Direct smear
Genome
Gram staining [under revision]
Growth curve
Hemolysis
Homogenization
Koch's postulates
Lancefield grouping of streptococci
Lipopolysaccharide (LPS)
Motility
Nomenclature of bacteria
Parameter
Pathogenicity
Plasmid
Pure culture
Pyogenic
Quorum sensing
Sepsis
Siderophore
Simple stain techniques
Spores
Streaking
Toxins
VBNC (Viable but nonculturable)
Virulence and virulence factors

Adherence [under revision]

Introduction

Adhesion in bacteriological contexts refers to the ability of bacteria to stick to surfaces (e.g. tissues). This ability can be more or less specific. For specific adhesion to take place, there must be a receptor on the surface and a ligand on the bacterium, which can bind to the surface. Bacteria use the so-called adhesins as ligands to attach to different receptors on cells in the host animal tissue. Adhesins are proteins or polysaccharides and their receptors can also be made of these components. Adhesins are important virulence factors because they contribute to the ability of bacteria to colonize different tissues.

Adhesin-receptor systems in bacteria

Fimbriae (= common pili) often function as adhesins and sometimes a particular polypeptide, which is localized at the tip of the fimbria is the actual ligand. Membrane proteins may also act as adhesins.

Updated: 2013-03-04.

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Anaerobic cultivation

Introduction

Some pathogenic bacteria are anaeribic and have to be cultivated in an oxygen-free atmosphere. The method of choice is dependent upon how anaerobic the bacterium to be cultivated is. There are strictly anaerobic bacteria, which cannot withstand oxygen at all, and there are aerololerant anaerobic bacteria, which will survive if the exposure to oxygen is not too long.

Strictly anaerobic bacteria

If you work with strict anaerobes, or if you have large amounts of samples to cultivate from, you may prefer a so-called anaerobic chamber where you work with rubber gloves sealed to the chamber. The anaerobic chamber maintains a constant temperature and the atmosphere may e.g. consist of nitrogen (N2) and carbon dioxide (CO2).

Aerotolerant bacteria

If you work with aerotolerant anaerobes maybe you prefer a so-called anaerobic jar where chemicals are used to absorb oxygen (O2) and generates CO2. There are commercial systems for this purpose. The anaerobic jar can be placed in thermostatic cabinet during the incubation.

Updated: 2013-02-25.

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Bacteriophages

Introduction Viruses are organisms which parasitize the host cell's protein synthesis machinery. Bacteriophages (phages or bacterial viruses) are viruses that infect and replicate in bacterial cells. Phages may have dsDNA, ssDNA, dsRNA or ssRNA as chromosome and the chromosome can be circular or linear. Phages have either a lytic or a lysogenic cell cycle.

Lytic phages

Lytic phages injects their chromosome into the bacterial host. To be able to do this, the phage has to adhere to specific receptors on the surface of the host bacterium. Then, the chromosome is replicated and phage proteins are synthesized by means of the host bacterial ribosome etc. When new phage progeny has formed, the bacterial host cell will lyse and the phage particles will find new bacterial host cells.

Lysogenic phages

Lysogenic (= temperate) phages does not lyse the host bacterium immediately, but its chromosome can instead be integrated into the bacterial genome and there it exist as a so-called prophage (endogenous phage). The prophage will then replicate during the bacterial cell division and is passed on to successive generations. The phage will exist as a prophage until the environment for the bacteria deteriorate. Then the prophage become active, form new phage particles and finaly lyse the host cell.

Lysogenic conversion

Some bacteria (e.g. Corynebacterium diphtheria, Clostridium botulinum, Shigella dysenteriae, Escherichia coli type VTEC and Streptococcus pyogenes) are pathogenic only if they carry a prophage. They are then said to have undergone lysogenic conversion and it is thus the genes of the prophage that encode important virulence factors.

Phages as diagnostic tools

Phages are not only species-specific, but in many cases also strain-specific and therefore, they can be used for subtyping of bacteria. Phagetyping is used for epidemiological studies of Salmonella enterica subsp. enterica. Phagetyping is perfomed by testing as a set of phage types and examine which of these can lyse the current salmonella strain. To perform the testing, a drop of bacteria is spread onto an agar plate, which is then allowed to dry on the surface. Then, small drops of phages with defined specificities are added. After incubation, the agar plate is inspected for plaques, which are formed where phages for which the bacterium is sensitive, have been applied. Exemples of other bacterial genera for which phage typing is used: Bacillus, Campylobacter, Clostridium and Staphylococcus.

Phage therapy

Since the problem of multi-drug resistant strains of bacteria increases worldwide, the interest in treating bacterial infectious diseases by phage therapy has increased. For this purpose, lytic phages are best suited. The method is still in the experimental stage, but many researchers believe that it has great potential in both human and veterinary medicine.

Updated: 2013-03-03.

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Biofilm

Bacteria that grow freely in liquid media are said to be planktonic, but some bacteria can also grow on solid substrates, forming a so-called biofilm. Biofilms can exist on live or dead surfaces and occur in nature, on materials in industrial processes and in different health care situations. Biofilms consist of population(s) of bacteria, which adhere to a surface and to each other and are enclosed in a network (matrix) of biopolymers. The formation of a biofilm starts with bacteria that adhere to a surface by means of e.g. fimbriae (pili) where they bind irreversibly and initially grow as a monolayer. Then they form several layers and start to produce some kind of a biopolymer (extracellular matrix) that often consists of the same material as the capsule, but in a looser structure. The biopolymer is made up of polysaccharides and is called glycocalyx (capsule). Dextran is one example of such a polysaccharide. Biofilms consist of one or more bacterial populations (species), glycocalyx, DNA and proteins.

A bacterial species that can not itself adhere to a surface, can often become attached to pre-existing bacterial glycocalyx and grow as a biofilm. Bacteria in biofilms are more resistant to antibiotics, detergents and phagocytosis than planktonic bacteria. Bacteria (Streptococcus spp.) can grow as biofilms on teeth (= plaques), on implants (e.g. heart valves), in plastic tubes, which transport nutrients etc. In patients with cystic fibrosis Pseudomonas aeruginosa may grow as a biofilm in the lungs. In biofilms, bacteria can communicate with each other by means of chemical signal substances (quorum sensing) to control gene expression in the whole population.

Link to a video montage on YouTube which is recommended: "What Are Bacterial Biofilms?"

Updated: 2013-03-03.

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Colony Forming Unit (CFU)

The number of bacteria in a liquid sample is often expressed as colony forming units per ml (CFU/ml). This value is determined by first making a ten-fold dilution series of the sample to be investigated. Then you take a known volume (e.g. by using a calibrated 1 µl plastic loop) from each tube and streak onto appropriate plates. After incubation, select a plate on which you recognize about 100 colonies, and by counting the colonies, you will get a good estimation of ​​the number of CFU/ml in the sample. Do not forget to multiply with the correct conversion factor. The reason for using the term CFU is that it is not certain that each colony originates from a single bacterial cell, because some bacterial species easily form aggregates in suspension cultures. Only living (or rather culturable) bacteria will give rise to colonies.

The number of bacteria (dead and alive) in a sample can be determined by counting them under a microscope in a calibrated chamber (a so-called Bürkner chamber).

For urinary tract infection (UTI), the term CFU is used and the amount of bacteria in the urine is used to be classified in the following way:

0 cfu/ml: no growth
<25 000 cfu/ml: sparse growth
25 000 - 100 000 cfu/ml: moderate growth
>100 000 cfu/ml: strong growth

Updated: 2013-03-03.

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Counting bacteria

Bacteria can be counted in different ways, and here are three fundamentally different methods:
  • Direct counting in a so called Bürkner chamber that can be placed under a microscope. The method is relatively uncertain and is not used that often.
  • Determination of CFU (Colony Forming Unit). Samples are taken from the culture is diluted and plated on agar plates, which are incubated until colonies can be observed. This method is relatively accurate, provided that dilution is done in a proper manner and the bacteria do not form aggregates in suspension cultures. Disadvantage: the answer is obtained only after approx. 24 h. See also Colony Forming Unit (CFU).
  • Spectrophotometric determination of light scattering. The method provides a relative measure of the number of bacteria, but can be calibrated with a standard curve. See Growth Curve.

    • Updated: 2013-03-03.

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Direct smear

Direct smear is perfermed by making a suspension of a clinical sample and smear it out directly onto a microscope slide without first making a bacterial cultivation. Then the sample is fixed and stained by simple stain techniques or differential stain techniques, to provide an indication of whether the sample contains pathogenic bacteria.

Updated: 2013-02-23.

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Genome

Introduction

The term genome refers to the complete set of genetic material in a cell. Genome size is usually expressed in Mb or Mbp (= mega base pairs). Thus, 1 Mbp = 1 000 000 bp. The size of the bacterial genome varies between 0.5 and 10 Mbp. Bacterial genomes comprise the chromosome(s) and possibly also plasmid(s). Bacteria are haploid, unlike higher organisms, which are diploid. Gametes of higher organisms are, however, also haploid. The complete genome sequences have been determined for about 4000 bacterial strains and there are approximately 14 000 ongoing genome projects for bacteria.

Chromosome

The chromosome represents the primary genetic material, which is essential for the bacterium. Bacteria in general have a circular chromosome, but there are exceptions (see below).

Plasmid

Plasmids (see also Genome above) are secondary genetic material, not always essential for the bacterium. Bacteria which carry plasmids generally have one or more circular plasmids, but there are also exceptions. Plasmids generally constitute up to 10% of the genome and they are replicated independently of the chromosome.

Exceptions

  • Some species within the genera Brucella, Burkholderia, Leptospira och Vibrio have two cirkular chromosomes
  • Species within the genus Borrelia have one linear chromosome (about 1 Mbp), which is relatively small.
  • Species within the genus Borrelia also have linear plasmids and these are essential for the bacterium.
  • Species within the genus Streptomyces have one linear chromosome, which is relatively big (about 10 Mbp).

Updated: 2013-03-03.

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Gram staining [under revision]

Introduction

Gram staining is a so called differential staining techniques, since one can distinguish two major groups of bacteria by this method. These two groups are gram positive and gram negative bacteria, which are stained purple and pink to red, respectively.

Principle

Gram-positive bacteria have a thick cell wall (peptidoglycan), which consists of several layers and can be likened to a network. Gram negative bacteria have a much thinner cell wall and also an outer membrane. Crystal violet (CV+), which is the primary dye binds to the negatively charged groups on the bacteria and stain them purple. Then iodine (I-) will be used to form a large complex (CV-I) with CV and thereby bind the stain to the bacterium. When Gram-positive bacteria are treated with the decolourizing solution (ethanol-acetone), the bacteria will be dehydrated and the colour retained. When Gram-negative bacteria are treated with the decolourizing solution the outer membrane will be dissolved and the thin peptidoglycan exposed, so that the CV-I complex is washed out. Then a counterstaining with safranin or basic fuchsin is performed to stain gram negative bacteria pink or red.

Method

... ... ...

Gram-positiva bacteria

Members of the phyla Firmicutes and Actinobacteria (exception: genus Mycobacterium).

Gram-negativa bacteria

Members of the phyla Proteobacteria (exception: some members of the order Rickettsiales), Cyanobacteria and Spirochaetes

Updated: 2013-03-08.

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Growth curve

Introduction

Bacteria multiply by binary fission (two identical daughter cells are formed upon the cell division). If the availability of nutrient is constant, and the physico-chemical properties of the culture medium does not change, they divide by the same speed all the time. This means that growth is exponential. The exponential growth phase (log phase) can not continue indefinitely, because the culture medium will become depleted of nutrients and the pH of the medium usually changes. When a bacterial culture is initiated in a liquid medium, it takes some time before the bacteria will start to grow, especially from clinical specimens or from hypothermic cultures and this phase of cultivation is known as the lag phase.

Generations time

The time required for the number of bacteria to double during cultivation is called generation time or doubling time and it can vary greatly for different bacteria. Escherichia coli, which is cultivated under optimum conditions, has a generation time of 20 min, whereas Mycobacterium avium subsp. paratuberculosis has a generation time of about 24 hours. This means in practice that if you spread these two bacteria on appropriate culture plates, you can easily see colonies of E. coli after one day, while colonies of M. avium subsp. paratuberculosis cannot be observed until after at least 3 months!

Growth curve

Growth curve Bacterial growth can be described by a so-called growth curve with four different phases: lag phase, log phase, stationary phase and death phase (= decline phase) (labelled A, B, C and D, respectively, in the figure). Note that the scale of the y axis is logaritmic. During the stationary phase bacteria die at about the same rate as they are formed during cell divisions, and in the death phase, bacteria die faster than they regenerate.

Construction of a growth curve

When a growth curve is constructed, you most often want to be able to follow the growth of bacteria in real time to know when to make e.g. addition of a substance, or when cultivation should be interrupted. The fastest and easiest method is to regularly collect samples from the culture and determine light scattering by spectrophotometry. With a spectrophotometer you normally determine absorbance at different wavelengths, but in a suspension (e.g. of bacteria) light scattering (OD = optical density) can also be measured. Light scattering is proportional to the number of bacteria per ml, and by means of a standard curve, one can determine the number of bacteria in absolute terms.

Updated: 2013-03-03.

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Hemolysis

Introduktion

Hemolysis (Brittish spelling: haemolysis) means that the red blood cells (erythrocytes) burst apart (hemolyse) and release the cell contents (hemoglobin). Some bacteria produce so-called hemolysins, which give them hemolytic capacity. Most hemolysins are proteins (enzymes or porins), but there are also other types of hemolysins like rhamnolipids and biological detergents (biosurfactants).

Protein hemolysins

Hemolysins are membrane distupting exotoxins which can be divided into two groups: toxins with enzymatic activity, and channel-forming toxiner (= porins).
Enzymatically active hemolysins are often lipases such as α-toxin of Clostridium perfringens, which is a phospholipase. When lipase cleaves lipids in plasma membranes of the host animal cells, the membrane will become fragmented and the cell contents leak out.
Porins are composed of subunits, but are secreted by the bacterium in monomeric form. In the cell membranes of the host animal, the monomers aggregate to channel-forming polymers (heptamers), which makes it impossible for the ion gradient across the plasma membrane of the host cell to be maintained and the osmotic pressure in the cell will increase until it lyses.

Function

A function of hemolysins is that the bacteria can utilize hemolysis to release and utilize nutrients from the host animal cells. Iron e.g., is essential to many pathogenic bacteria, but is only present in very low concentrations outside the cells. If the bacteria have access to free hemoglobin, it can utilize the iron, which is bound to the heme groups of hemoglobin. Hemolysins do not act only on erythrocytes, but can also lyse other types of cells.

Identification of bacteria based on haemolysis

By cultivation on blood agar, bacteria can be differentiated based on their capacity to secrete hemolysins. The hemolysis will cause a clearing zone of the blood agar around the colonies. Bacteria can cause different types of hemolysis:

  • α-hemolysis, which means an incomplete clearing (green haemolysis).
  • β-hemolysis, which means a complete clearing.
  • Double hemolysis of some staphylococci consisting of an inner α-hemolysis zone and an outer β-hemolysis zone (see also below).
  • No hemolysis, which is sometimes referred to as γ-hemolysis, which may seem illogical.
Note that the α-hemolysin of staphylococci causes complete hemolysis, whereas their β-hemolysin causes incomplete hemolysis.
The capacity to produce hemolysins may vary between different strains of a particular bacterial species.

Updated: 2013-03-06.

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Homogenization

Stomacker In order to cultivate bacteria from certain types of samples (including food and feed) it is important to disperse the sample in the dilution broth without damaging the bacteria. A Stomacher® is an apparatus used for homo­geni­sation of samples in food micro­biology. A large amount of viable microorganisms can be released from different kinds of food samples by this method. The apparatus does not have to be sterilized because the samples are contained in sterile plastic bags to which sterile medium is added.

A. The homogeniser, which is loaded with a plastic bag containing the sample and culture fluid
B. Rack for the plastic bags during the incubation
C. Rack, which is used during the weighing of sample material and addition of culture medium
D. Sterile plastic bags in the homogenizer and for the incubation

Click on the image to enlarge it.

Updated: 2013-02-26.

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Koch's postulates

Introduction

Robert Koch was a German physician (1843-1910), who was interested in the relationship between microorganisms and disease. Koch formulated four criteria (Koch's postulates), which must be met to prove that a particular microorganism has caused a certain disease (viruses however, require other criteria).

Koch's postulates

  1. The microorganism must/should be detected in large numbers in all individuals who suffer from the disease, but it must/should not be present in healthy individuals
  2. The microorganism must/should be cultivated in pure culture from samples coming from the sick individual.
  3. The cultured microorganism must/should cause the sama disease in healthy individuals (laboratory animals).
  4. The microorganism must/should then be cultivated from or detected in the diseased laboratory animal.

In the original version of the postulates must was used, but with today's knowledge, one must use should as there are many exceptions. The first criterion had to be abandoned when it was discovered that there are asymptomatic carriers of certain microorganisms (subclinical infections). The second criterion must sometimes be abandoned because there are microorganisms that cannot be cultivated. The third criterion is not always valid because external factors can affect the results of an experimental infection.

Conclusion

If all criteria are met, a relation between microorganisms and disease has been proven, but if not all criteria are met, then it may still be a connection.

A number of new criteria to prove a relationship between microorganisms and disease was published in 1996 (Fredricks and Relman, Clin. Microbiol. Rev. 9:18-33). These criteria are based on detection of specific DNA sequences associated with disease.

Updated: 2013-03-08.

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Lancefield grouping of streptococci

Streptococci are sometimes classified in so-called Lancefield groups after the American microbiologist Rebecca Lancefield (1895 – 1981), who developed a system for serological classification based on the carbohydrate composition of the cell wall. The different groups are called Lancefield groups A to V (except I and J). There is also a group NG (= non-groupable).

Updated: 2013-03-06.

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Lipopolysaccharide (LPS)

Introduction

Lipopolysaccharides (LPS), which are also known as lipoglycans, are only present in the outer membrane of gram negative bacteria. LPS is a so-called endotoxin (se även toxin nedan) and the toxicity is associated to lipid A (see below).

Structure

LPS is an amphipathic molecule, i.e. it has both hydrophilic (water loving) and hydrophobic (water repellent = lipid loving) regions. The hydrophobic portion (hydrocarbon chains) anchors LPS in the outer lipid layer of the bacterial outer membrane and the hydrophilic region (charged groups) points outward against the bacterial environment. Chemically, LPS consists of a lipid moiety and a polysaccharide moiety. The lipid moiety comprises lipid A, which is a phosphorylated glucosamine disaccharide with several (about 6) linked hydrocarbon chains, which constitute the hydrophobic portion of the molecule. The carbohydrate moiety consists of a so-called core oligosackaride (core antigen or R antigen), which is directly bound to lipid A. The polysaccharide (O-polysaccharide, O-antigen or somatic antigen) is then bonded to the R antigen.

Specificity

Thanks to the diversity, found in LPS from various gram-negative bacteria, its antigenic properties can be used for typing and subtyping of bacteria. The antigenic properties will also vary in different parts of LPS:
  • Lipid A is often family-specific. In for instance the family Enterobacteriaceae, there is almost no variation in the structure of lipid A.
  • The R antigen is often specific to the genus, i.e. no significant variation occurs in this part within a single bacterial genus.
  • The O-antigen is not even species specific, i.e. considerable variation occurs even within a species and this provides opportunities for subtyping by serological methods. Thus, one can distinguish between different strains of the same species, which makes it possible to use serology for epidemiological studies.

Effects on the host animal

Animals (including humans) are constantly exposed to small amounts of LPS in the blood circulation because of the turnover of intestinal gram negative bacteria and thus the innate immune system is contiuously stimulated. Exposure to large amounts of LPS, as during for instance sepsis, will cause release of cytokines, leading to fever and inflammation. At toxic concentrations of LPS, blood clots form in the capillary system, which in turn can lead to life-threatening conditions.

Updated: 2013-03-06.

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Motility

Introduction

Many bacteria are motile and they can migrate by utilizing mechanisms based on different principles. Motility mechanisms have been developed in bacteria in order for them to be to be attracted or repelled by certain stimuli. Motility is a feature, which is used for characterization and identification of bacteria and methods have, therefore, been developed to detect motility. Bacterial locomotion must be distinguished from so-called Brownian molecular motion, which is random and depends on the thermal motion of water molecules, which can push the bacteria so that it is perceived as if the bacteria move under the microscope.

Swimming movement by means of flagella

Bacteria can have flagella, which may be one or several in number, and which act as propellers and allow the bacteria to move in a predetermined direction. Very simplified, you can say that the flagellum consists of a moving filament, which is linked to a molecular engine (basal body) in the bacterial envelope via a hook. The flagellum consists of many subunits of the protein flagellin, which form a hollow and flexible cylinder. The molecular engine, which is built up by protein subunits, is driven by the proton gradient (or a Na+ ion gradient) over the cell membrane and can get the filaments to rotate clockwise or counterclockwise. This rotation causes the bacteria to swim in a certain direction and to tumble, respectively. The direction is dependent on outer stimuli and during tumbling, the bacteria can change direction of the movement.

Bacteria within the phylum Spirochaetes have so-called periplasmic flagella (endoflagella or axial filaments), which are localized in the periplasmic space between the cell membrane and the outer membrane. This arrangement result in a screw like motility (or flat-wave motility), which makes it possible for these bacteria to move in highly viscous material (like mucus).

Twitching motility by means of type IV pili (fimbria)

Bacteria which have so-called type IV pili can move by using the external ends of the pili, which have hooks, and can adhere to a solid substrates like the surface which the bacteria colonize or to other bacteria. When the pilus contracts, the bacteria are pulled forward. Movement produced by type IV pili is typically jerky, and thus it is simply called twitching motility. Pseudomonas aeruginosa has this twitching motility.

Gliding motility on surfaces

Some bacteria can glide on wet surfaces, but the molecular mechanisms are incompletely understood. Examples of bacteria, which have this ability are: members of the phylum Cyanobacteria and the genera Flavobacteria and Mycoplasma.

Motility by utilizing the cytoskeleton of the host cell

Some pathogenic bacteria can move inside the host cell by using its cytoskeleton. The cytoskeleton is normally used to move organelles inside the cell. By stimulating actin polymerization at one pole of the host cell, these bacteria can form a kind of tail, which pushes them through the cytoplasm of the host cell. Examples of bacteria that can use this mechanism are Listeria spp. and Shigella spp.

Updated: 2013-03-06.

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Nomenclature of bacteria

Introduction

Nomenclature of bacteria refers to naming and bacteria and other organisms are named according to the binomial system, which was introduced by Carl Linnaeus (1674-1748). This means that a bacterium has a species name, which is composed of a genus name that tells you to which genus it belongs and a species epithet which, together with the genus name, is unique to the bacterium. An example of this is Moraxella bovis, where the genus name indicates that the bacterium belongs to the genus Moraxella and the species name indicates that the bacterium has been isolated from cattle. The genus name and the species epithet form together the scientific name of the species, which is always written in italics. Bacterial names are international and Latin or latinized Greek are used to form the name. If misunderstandings cannot occur, you can abbreviate the genus name after it has been written for the first time in a text, e.g. M. bovis. However, note that there are also bacteria called Mycoplasma bovis and Mycobacterium bovis.

There are strict international rules for how bacteria should be named and these rules are published in a book named:" International Code of Nomemclature of Bacteria". In order to get a proposed name accepted, a scientific paper on the proposed species must be published and approved by an international taxonomy committee.

Trivial name

Trivial names are often used as a simplified way of naming a bacterial genus. A trivial name should neiter be written with capital first letter nor in italic. Examples of trivial names are: lactobacilli, mycobacteria, salmonella, staphylococci and streptococci. The scientific names for these groups are: genus Lactobacillus (or Lactobacillus spp.), genus Mycobacterium (or Mycobacterium spp.), genus Salmonella (or Salmonella spp.), genus Staphylococcus (or Staphylococcus spp.), genus Streptococcus (or Streptococcus spp.), respectively.

If you refer to a specific bacterial species, a trivial name refering to a complete genus should never be used.

Subspecies, biovars and serovars

Sometimes there is a need to divide bacterial species into subspecies, because they are too closely related to be regarded as different species, but too distantly related to be regarded as the same species. In this case a subspecies is introduced by adding a subspecies epithet and write subspecies (subsp. or ssp.) in front of it. An example of this is Streptococcus equi subsp. equi. When you divide a species into several subspecies, the original species always gets the same subspecies epithet as the species epithet.

There is often a need to divide species and subspecies in different biovars (bio­logi­cal variants) or different strains, but this is not strictly regulated, which means that researchers themselves can name their strains or biovars. One type of biovar is serovar (serological variant), by which various surface antigens can be identified with specific antibodies. Contact tracing and epidemiology is based on identification of different variants of the same bacterial species.

Salmonella nomenclature

A bacterial subspecies that occurs in several thousand different serovars is Salmonella enterica subsp. enterica. A common serovar is Dublin and if you you want to write the complete and correct name of the bacterium, it becomes Salmonella enterica subsp. enterica serovar Dublin. Please note that the name of the sero­var is capitalized, but not italicized. If the name appears in several places in the text, you can write S. enterica subsp. enterica serovar Dublin. However, because even this abbreviated writing is rather lengthy, it has been agreed that it is acceptable to simply write Salmonella Dublin, except on the first occurrance in a text, where the name must be given in full.

You can read more about naming of salmonellas on VetBact at Salmonella spp. and Salmonella enterica.

Updated: 2013-03-06.

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Parameter

Parameter is a term, which is usually used to identify the variable and measurable characteristics, which define a system. The system may e.g. consist of a bacterial culture and examples of parameters are: number of added bacteria, growth temperature, incubation time, salt concentration, glucose concentration, CO2 concentration, etc.

Testing parameter in food microbiology refers to standardized routine methods for the determination of e.g.: number of slow-growing bacteria, intestinal enterococci, culturable microorganisms etc.

Updated: 2013-02-26.

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Pathogenicity

Introduction

The ability of a microorganism to cause any kind of damage (i.e. disease) to the host animal is called pathogenicity and microorganisms that have this ability are called pathogenes (or pathogenic organisms). Pathogenic is an "all-or-none-characteristic", i.e. a microorganism are either pathogenic or non-pathogenic in a given host animal. Virulence is not synonymous with pathogenicity, but describes the degree of damage that the pathogen has caused. A highly virulent bacterium is very contagious and/or gives severe symptoms.

Obligate or opportunistic pathogens

A microorganism may be an obligate pathogen or an opportunistic pathogen. An obligate pathogen can be found in the host animal only in connection with disease. Microorganisms, which are found in healthy host animals, but which may cause a disease in certain circumstances are known as opportunistic pathogens. Such circumstances may be an immunocompromised host, other infection, tissue damage, etc.

Characteristics that make a bacterium pathogenic

  • Production of toxin.
  • Production of adhesin.
  • Production of capsule.

Updated: 2013-03-06.

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Plasmid

Plasmids constitute secondary genetic material in bacteria, which can be used if the need arises (see also Genome above). Plasmids can be present in one or several copies in a cell, as they replicate independently of the chromosome. A bacterium may carry multiple different plasmids.

Function

Plasmids may contain genetic information, which is necessary for:
  • Antibiotic resistance.
  • Synthesis of antibiotics such as streptomycin in Streptomyces spp.
  • Synthesis of bacteriocins that are toxic to the strains of the same bacterial species, which do not contain the same plasmid. Example: colicines of E. coli.
  • Conjugation [e.g. F (fertility) plasmid in E. coli].
  • Synthesis of enzymes that degrade organic substances.
  • Virulence genes (see Virulence factors), such as those of the genera Shigella, Salmonella and Yersinia. Virulence genes can also be found in so-called prophages, which is another type of secondary genetic material.

Practical use

Plasmids have been of great use in molecular biology including cloning of genes. Genetically modified plasmids, which contain only a few genes and a suitable cloning site, are then used.

Updated: 2013-03-06.

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Pure culture

Introduction

A clinical sample seldom contains bacteria in pure culture, but they are usually found in a mixed flora. Thus, the pathogenic bacterial species is often isolated in combination with the normal bacterial flora during a bacterial infectious disease. To identify key bacteria in clinical samples, you have to have them in pure culture. A pure culture thus contains only one species of bacteria, and this can be accomplished by streaking (see below) onto agar plates.

Updated: 2013-02-25.

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Pyogenic

A pyogenic (= suppurative or purulent) bacterium is a pus-forming bacterium. If mucus is also generated, the bacterium is called mucopurulent. Examples of pyogenic bacteria are Burkholderia mallei, Klebsiella pneumoniae, Staphylococcus aureus, Sta. epidermidis, Streptococcus pyogenes och Str. pneumoniae.

Pyogenic bacteria may cause pyemia (see sepsis below).

Updated: 2013-03-06.

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Quorum sensing

Introduction

Quorum sensing is a system for signaling and response in a population of organisms (e.g. bacteria), regulated by the population size. In other words, the gene expression (= protein synthesis) of certain proteins can be regulated in response to changes in population density. Quorum comes from the Latin and means "of them", which refers to the minimum number present, as required for taking a decision.

Why do bacteria communicate with each other?

If very few bacteria are present in a particular area, it is a waste of energy to produce and secrete e.g. certain enzymes and, therefore, gene expression is regulated by quorum sensing. Formation of biofilm (see above) is also regulated by quorum sensing. Synthesis of the constituents of a biofilm is initiated when the bacterial population density has reached a certain level.

How do bacteria communicate with each other?

Bacteria use quorum sensing if necessary, to regulate gene expression in relation to the population size. The bacterium releases chemical messengers in the form of complex organic molecules (polypeptides in gram positive and N-acyl homoserine lactones in gram-negative bacteria) to achieve this. The concentration of signaling molecules is not high enough for the bacteria to communicate with each other in a population of planktonic bacteria (see Biofilm above). However, in a biofilm it is, and therefore they can communicate.

Links

Updated: 2013-03-06.

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Sepsis

Sepsis (blood poisoning) is a potentially deadly medical condition with a whole-body inflammatory state [systemic inflammatory response syndrome (SIRS)], which is usually caused by a bacterial infection.

Septicemia (septicaemia) is a related medical term referring to the presence of pathogenic organisms that multiply in the bloodstream, leading to sepsis.

Bacteremia (bacteraemia) is transiently presence of bacteria in the blood and this term is not equivalent to sepsis.

Pyemia (pyaemia) is a form of septicemia, which results in widespread abscesses of a metastatic nature. Pyemia is usually caused by the presence of pyogenic (pus-forming) bacteria in the blood.

Updated: 2012-12-11.

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Siderophore

Introduktion

The word siderophore originates from Greek and means iron carrier. Siderophores are low molecular weight substances that have very high affinity for iron (Fe3+) and they bind iron by so-called chelation. Iron is essential for almost all forms of life. Many bacteria can secrete siderophores, which allows them to absorb iron even in an environment where the concentration of free iron is very low. In mammals, iron is tightly bound to various proteins (e.g. ferritin, lactoferrin, hemoglobin and transferrin) and therefore, pathogenic bacteria bind iron in the form of soluble complexes with siderophores. Siderophores are considered as virulence factors.

Examples of siderophores

Bacterium
 Siderophore
Bacillus anthracis
 Bacillibactin
Bacillus subtilis
 Bacillibactin
Escherichia coli and some other enteric bacteria ...
 Enterobactin
... e.g. Salmonella spp.
 Enterobactin
Some species within the genus Mycobacterium (e.g. M. tuberculosis) Mykobactin
Pseudomonas aeruginosa Pyochelin och pyoverdine
Yersinia enterocolitica Yersiniabactin
Y. pestis Yersiniabactin
Y. pseudotuberculosis Yersiniabactin


Updated: 2013-02-03.

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Simple stain techniques

Simple stain methods are methods that utilize the fact that the negatively charged cytoplasm of bacteria attracts positively charged dyes like crystal violet and methylene blue. This can be used for rapid staining of specimen on microscopic slides after fixation with ethanol.

By simple stain techniques, it is possible to determine whether a sample contains rods or cocci, but not if they are Gram-positive or Gram-negative. To determine whether the bacteria are Gram-positive or Gram-negative, one can use Gram staining, which is a differential stain method.

Updated: 2013-02-24.

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Spores

Introduction

Spores in bacteria is not the same as spores of fungi. Bacteria do not use spores to reproduce, but to survive adverse conditions (lack of nutrients, extreme pH, high temperature etc). Some bacteria may switch to a resting state by forming spores.

Endospores

Endospores are formed, as the name suggests, inside the bacterial cell. Endospores are highly resistant and can be formed by members of the phylum Firmicutes. The genera, which are most important in veterinary medicine are Bacillus and Clostridium. Members of the genus Paenibacillus can also form endospores. In each bacterial cell only one spore is formed and it can survive without access to nutrients. Endospores can withstand high and low temperatures, dehydration, chemical disinfectants and UV radiation, and the reason why they are so resistant is that they contain almost no water, and that the cell wall contains dipicolinic acid. The spores also contains much calcium (Ca) and when Ca2+ is pumped into the spore, the water is pumped out. In addition to the envelope (cortex) the spore contains primarily just DNA, ribosomes and polymerases. This is sufficient for the spores to germinate i.e. develop into bacteria again when the conditions become favorable.

Treatment with moist heat (+121°C) for 15 minutes is required to kill endospores, since they are so resistant.

Use in diagnostics

Endospores may be of importance for identification of bacteria. The position of the spore in the mother cell can give information about possible bacteria. B. cereus, B. subtilis and C. tetani for instance, have a central, subterminal and terminal spore, respectively.

Länk

Video clip at YouTube that is recommended: "Bacterial Spore Formation".

Akinetes

The orders Nostocales and Stigonematales of the phylum Cyanobacteria form so-called akinetes, which is a type of resting stage for these bacteria. Akinetes is not the same as endospores and they are not as resistant, but in the form of akineter these cyanobacteria survive the cold (winter season) and dehydration.

Exospores

The genera Actinomyces and Streptomyces of the phylum Actinobacteria can form a type of spores referred to as exospores. Exospores are formed by budding of the mycelium like structures (filaments), which these bacteria exhibit during growth. Exospores are not as resistant as endospores and therefore not of the same clinical significance. They also have a completely different structure.

VBNC

Is actually something different from spores, see VBNC (Viable but nonculturable) below.

Updated: 2013-03-05.

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Streaking

Agar platesStreaking is a technique used in bacteriology for isolating individual bacterial species or strains from a sample containing a mixed bacterial flora. A sterile inoculation loop (plastic or platinum), which has been dipped into the sample, is used to streak on 1/3 (alt. 1/4) of an agar plate. Then you take a new loop and streak from the first third to the next third of the plate. This is then repeated once (or twice). In this way you get a significant decrease of bacteria between each third (or fourth) of the plate and the chance is good that somewhere on the plate, you can find individual colonies of the bacterium or bacteria you want to isolate. The panel to the right shows a streaking of Staphylococcus aureus subsp. aureus in three steps on a bovine blood agar plate. The two images (A and B) show the same plate photographed with lighting from above and in backlight, respectively. Note that on plate B it is possible to see the traces of the streaks even when bacterial colonies cannot be observed.

A colony, originating from a streaking, generally form a clone because most probably it originates from a single bacterial cell. There are, however, exceptions because some bacteria grow in the form of aggregates rather than as single cells. For bacteria that tend to swarm, plates which reduces the risk (for example, CLED agar for soma bacteria) should be used.

Updated: 2013-03-05.

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Toxins

Introduction

Bacterial toxins are important virulence factors and they are usually classified as exotoxins (exo = outside) or endotoxins (endo = inside). Exotoxins are actively synthesized and secreted, whereas endotoxins are part of the bacteria and are released upon bacterial death and lysis. Most endotoxins are localized to the bacterial envelope and often, only lipopolysaccharides (LPS) of the outer membrane of gram negative bacteria are affiliated to thid group (see also lipopolysaccharide above). Endotoxins are heat stable.

Exotoxins

Exotoxins are typically heat sensitive (heat labile) proteins, but some are heat stable polypeptides. Exotoxins may be formed by both gram positive and gram negative bacteria. Among bacterial exotoxins, some of natures most potent toxins are found. The lethal dose for humans of e.g. the botulinum toxin is only 1-2 ng (1 ng = 0,000 000 001 g) per kg body weight at intraveneous administration. Thus, the botulinum toxin is approximately 6 000 000 times more toxic than the rattle snake venom.

Exotoxins can in turn be classified in various ways, e.g. according to:

  • The tissue they affect: e.g. enterotoxins, hepatotoxins, leukocidins and neurotoxins.
  • The bacterium that produces the toxin: e.g. anthrax toxin, botulinum toxin, cyanotoxin, shiga toxin, staphylococcal toxin and tetanus toxin.
  • The structure of the toxin: e.g. AB toxins, which consist of two different protein subunits, A and B. A and B refers to active and binding, respectively, i.e. the actions of the subunits on the target cell. There are also AB5-toxins, which consist of 5 identical subunits (B) and one unique subunit (A), which has a different structure.
  • The action of the toxin: e.g. invasins, hemolysins, toxins with enzymatic activity and channel forming toxins. Invasins make it easier for the bacteria to invade the tissue of the host animal and hemolysins can lyse the erythrocytes (and other cells) of the host animal (see hemolysis above). Toxins with enzymatic activity can be lipases, which split phospholipids in the cell membrane which in turn will cause the host cell to be fragmented (see also hemolysis above). Channel forming toxins (= porins) will get the ion gradient over the cell membrane to collapse and that will also cause fragmentation of the host cell (see also hemolysis above).
  • The target organelle within or outside the host cell may be e.g. extracellular matrix, the plasma membrane, the cytoplasm and the immune system. Toxins targeting extracellular matrix are often enzymes (hyaluronidase, collagenase and elastase etc.), which can digest the constituents. Toxins targeting the plasma membrane affect its permeability and interfere with its transmembrane signaling system. Toxins targeting components in the cytoplasm also interfere with signaling systems or cytoskeleton. Toxins that cause dysfunctions in the immune system are so-called superantigens.
The different classification systems are unfortunately a source of confusion, because one toxin can have different names depending on the applied classification system. The botulinum toxin e.g. is both a neurotoxin and an AB toxin. Abbreviations are often used and the botulinum toxin for instance can be designated BoNT.

A toxoid is a protein toxin, which has been denatured (by e.g. heat or chemical treatment) and has, therefore, lost its toxicity. A toxoid retains, however, its antigenic properties and can, therefore, be used in vaccines.

Endotoxins

LPS does not exist in gram positive bacteria, but except LPS, there are some other endotoxins and one example is the Cry protein in Bacillus thuringiensis, which is a so-called δ-endotoxin. Endotoxins are in general much less toxic than exotoxins.

Secretion systems

Bacteria have complicated secretion systems to be able to export proteins to the surrounding or to the cytoplasm of cells of the host animal. Proteins, which are exported are often toxins. Information about secretion systems will be included in the term list.

Updated: 2013-03-05.

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VBNC (Viable but nonculturable)

VBNC refers to bacteria that are viable but not culturable. These bacteria have due to adverse conditions entered into a state of very low metabolic activity, and therefore they do not divide any longer. This condition is not as resistant as spores, but they can exist as VBNC for at least one year. Under the right conditions, VBNC bacteria may return to the normal state and become culturable again.

Examples of bacterial genera and species, which may enter into the VBNC state: Aeromonas, Burkholderia, Campylobacter, Enterobacter, Entercoccus, Escherichia coli, Francisella, Helicobacter, Klebsiella, Legionella, Listeria, Mycobacterium, Pasteurella, Pseudomonas, Salmonella, Serratia, Shigella, Streptococcus and Vibrio.

Updated: 2013-02-26.

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Virulence and virulence factors

Introduction

Virulence is not synonymous with pathogenicity (see also pathogenicity above), but describes the degree of damage that the pathogen has caused the host animal. A highly virulent bacterium is very contagious and/or gives severe symptoms. Thus, the infectious dose (ID) is lower for a high-virulent than for a low-virulent microorganism.

Virulence factors

Virulence factors are the components that bacteria produce in order to:
  • Colonize some tissue of the host animal (adhesins).
  • Invade tissues (tissue-degrading enzymes, see Toxins).
  • Invade and get out the cells of the host (applies for intracellularbacteria).
  • Escape the immune system of the host animal (by producing a capsule or by means of phase variation, which refers to a change in expression of surface proteins).
  • Inhibit the immune system of the host animal (by digesting the antibodies of the host animal with specific proteases).
  • Utilize nutrients from the host cells (by means of e.g. siderophores).
  • For some of the bacterial toxins (e.g. botulinum toxin and tetanus toxin), the functions for the bacteria are not known, i.e. which benefits the bacteria may have from them. However, these toxins are still very important virulence factors.
Virulence genes are the genes encoding for virulence factors or components required for the synthesis of virulence factors.

Updated: 2013-03-06.

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