Bacteriology

 BACTERIOLOGY

Bacteriology is a branch of microbiology that is concerned with the study of bacteria (as well as Archaea) and related aspects. It's a field in which bacteriologists study and learn more about the various characteristics (structure, genetics, biochemistry and ecology etc.) of bacteria as well as the mechanism through which they cause diseases in humans and animals.

Bacteriology played an important role in the development of the fields of molecular biology and genetics. This subdivision of microbiology involves the identification, classification, and characterization of bacterial species. A person who studies bacteriology is a bacteriologist.

BACTERIA: Bacteria are small prokaryotic cells (a unicellular organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle). Prokaryotes are divided into two domains, Bacteria and Archaea. Prokaryotes reproduce without fusion of gametes. Bacteria and Archaea reproduce through asexual reproduction, usually by binary fission.

Most prokaryotes are between 1µm and 10 µm, but they can vary in size from 0.2 µm (Mycoplasma genitalium) to 750 µm (Thiomargarita namibiensis).

General characteristics of bacteria: 

They are prokaryotic 

They are simplest of all microbial cells 

Bacteria are single celled organisms

They have distinctive cell wall which contain peptidoglycan 

They are measured in unit called micrometer 

Bacteria lack a true nucleus but have a region called the nucleroid region, i.e. DNA is free floating 

They may have additional DNA called a plasmid 

Their reproduction is by binary fission 

They are extremely diverse and numerous in soils and waters.

Morphology:

Bacteria are microscopic unicellular organisms. The unit of measurement of bacteria is the micrometer (µm); i.e. 1mm is equal to 1000 microns. Morphological classification of bacteria is based on the following types of shapes of cells.

Cocci (Singular: Coccus): these are round or oval bacteria measuring about 0.5 – 1.0 µm in diameter. When multiplying, cocci may form pairs, chains or irregular groups.

Cocci in pairs are called diplococcic, e.g. meningococci and gonococci.

Cocci in chains are called streptococci, e.g. Streptococcus pyogenes

Cocci in irregular groups are called staphylococci i.e. bunch of circular microbes e.g. Staphylococcus aureus.

Gram reaction: Staphylococci and Streptococci are Gram positive, whereas diplococcic can be Gram positive or Gram negative

Tetracocci (Tetrad): cocci in group of 4 cells e.g. Tetracoccus cechii

Sarcinae: packet of 8 or more cells e.g. Sarcina aurantiaca, Sarcina lutea

Bacillus (Rods): These are rod-shaped (stick-like bacteria) in structure about 0.2 to 100µm in length. They may occur in pairs as in diplobacilli or in chains as in Streptobacilli species, or form branching chains e.g. lactobacilli, mass together e.g. Mycobacterium leprae

The rods of the genera Bacillus and Clostridium are able to form resistant spores when conditions for vegetative growth are unfavorable. Many rods are motile having a single flagellum, or several flagella, at one or both ends or surrounding the entire organism.

Gram reaction: Many rods are Gram-negative such as the large group of enterobacteria. Gram-positive rods include Clostridium species, Corynebacterium species, Bacillus anthracis and Listeria monocytogenes

Vibrios

These are small slightly curved rods (comma-shaped), less than one complete turn or twist, as seen in Vibrio cholera. Measuring 3-4 µm in length by 0.5 µm in width. Most vibrios are motile with a single flagellum at one end.

Gram reaction: Vibrios are Gram-negative 

Fusiform

These organisms (bacteria) are spindle-shaped, that is wide in the middle and tapers at both ends e.g. as seen in Sarcina species, Fusobacterium necrophorum.

Spirilla (Spirillum): these are small, regularly coiled, rigid organisms measuring about 3-4 µm in length. Each coil measures about 1 µm. Spirilla are motile with groups of flagella at both ends. An e.g. of a spirillum is Spirillum minus.

Gram reaction: Spirilla are Gram-negative

Spirochetes: These are flexible, coiled, motile organisms. Most are not easily stained by the Gram method. Treponema pallidum.

Actinomycetes: These resemble fungi in structure because they are filamentous form of bacteria as seen in Actinomyces israelii.

Some important human bacterial pathogens

s/n

Organism

Disease

1

Staphylococcus aureus

Septicemia, food poisoning, abscesses, carbuncles 

2

Streptococcus pyogenes

Tonsilitis, erysipelas, scarlet fever

3

Streptococcus pneumonia

Pneumonia, meningitis, septicemia

4

Neisseria meningitides

Meningitis, septicemia

5

Neisseria gonorrhoeae

Gonorrhoea

6

Escherichia coli & other coliforms

Urinary tract infection, septicemia, pyogenic infections

7

Salmonella typhi, paratyphi A,B, and C

Enteric fever

8

Salmonella species

Food poisoning

9

Shigella spp.

Dysentry

10

Vibrio cholera

Cholera

11

Proteus spp

Urinary tract and wound infection

12

Haemophilus influenza

Meningitis, pneumonia, epiglottitis, septicemia

13

Bordetella pertussis

Whooping cough

14

Mycobacterium tuberculosis

Tuberculosis

15

Clostridium tetani

Tetanus

16

Bacillus anthracis

Anthrax

17

Corynebacterium diphtheria

Diphtheria

18

Treponema pallidum

Syphilis

19

Mycobacterium leprae

Leprosy

20

Chlamydia spp

Trachoma, pneumonia, genital tract infection

Meaning of some microorganisms

Escherichia coli- Named after Theoder escherich in 1888; found in colon.

Haemophilus ducreyii– Haemo-blood, phil-love. Named after Auguston Ducrey in 1889.

Neisseria gonorrhea- Named after Albert Neisser in 1879; cause the disease gonorrh oea.

 Saccharomyces cerevisiae- Saccaro=sugar, myco=mold, cerevisiae=beer or ale.

 Staphylococccus aureus- aureus= golden, staphylo=clustrer, Kokkus= berry

Streptococcus lactis- strepto=twisted chain, kokkus=berry, lacto=milk

Rhizopus nigricans- Rhizo= rod like, nigricans=black colour

Penicillum notatum- Penicil=tutt like (pencil) apperance, notatum= spores easily spread in air.

Streptococcus pyogens- strepto=twisted chain, kokkus=berry, pyogens= from pus

Klebsiella pneumoniae- kleb= honours of discovered, pneunmoniae= disease it cause

Salmonella typhimurium- salmon= honours of Daniel Salmon, Typhimurium=causes stupor( typhi ) in mice.

Trypanosoma cruzi- Trypane=borer, soma=body, cruzi=honour of epidemiologist oswaldocruz

CHEMICAL COMPOSITION OF THE BACTERIAL CELL WALL

The bacterial cell wall is a complex, mesh-like structure that in most bacteria is essential for maintenance of cell shape and structural integrity. Bacteria possess cell wall which is made of peptidoglycan layer (murein)- is a polymer consisting of sugars and amino acids that forms a mesh-like outside the plasma membrane of most bacteria, forming the cell wall. The sugar component consists of alternating residues of β-(1,4) linked N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). There are 4-5 amino acids attaching to N-acetylmuramic acid; which is tetra to penta peptide linking with muramic acid.

Gram-positive cell wall

The cell walls of gram positive bacteria are composed predominantly of peptidoglycan. In fact, peptidoglycan can represent up to 90% of the cell wall, with layer after layer forming around the cell membrane. The NAM tetrapeptides are typically cross-linked with a peptide interbridge and complete cross-linking is common. All of this combines together to create an incredibly strong cell wall. In the Gram-positive Bacteria (those that retain the purple crystal violet dye when subjected to the Gram-staining procedure), the cell wall consists of several layers of peptidoglycan. Running perpendicular to the peptidoglycan sheets is a group of molecules called teichoic acids which are unique to the Gram-positive cell wall.

Gram-negative cell wall

The cell walls of gram negative bacteria are more complex than that of gram positive bacteria, with more ingredients overall. They do contain peptidoglycan as well, although only a couple of layers, representing 5-10% of the total cell wall. What is most notable about the gram negative cell wall is the presence of a plasma membrane located outside of the peptidoglycan layers, known as the outer membrane. In the Gram-negative Bacteria (which do not retain the crystal violet), the cell wall is composed of a single layer of peptidoglycan surrounded by a membranous structure called the outer membrane. The outer membrane of Gram-negative bacteria invariably contains a unique component, lipopolysaccharide (LPS or endotoxin), which is toxic to animals. In Gram-negative bacteria the outer membrane is usually thought of as part of the cell wall.

CYTOPLASMIC MEMBRANE

The cytoplasmic membrane, also called a cell membrane or plasma membrane, is about 7 nanometers (nm;1/1,000,000,000m)  thick.

It lies internal to the cell wall and encloses the cytoplasm of the bacterium.

It is the most dynamic structure of a prokaryotic cell.

Structure of cell membrane

The structure of bacterial plasma membrane is that of unit membrane, i.e., a fluid phospholipid bilayer, composed of phospholipids (40%) and peripheral and integral proteins (60%) molecules.

The phospholipids of bacterial cell membranes do not contain sterols as in eukaryotes, but instead consist of saturated or mono unsaturated fatty acids (rarely, polyunsaturated fatty acids).

Many bacteria contain sterol-like molecules called hopanoids (are diverse group of penta cyclic triterpenoid lipids mainly produced by bacteria).

The hopanoids most likely stabilize the bacterial cytoplasmic membrane.

Bacterial Flagella

Flagella (singular. Flagellum): these are hair like, slender filaments that originate from the cytoplasm. They functions as organs of motility. They are therefore seen only in organisms that are motile. Based on their location on the cell flagella may be polar or lateral.

Polar: at one end or both ends of bacterium

Lateral: along the sides of the bacterium

Types of Flagella

Monotrichous: one flagellum at one pole e.g. Vibrio cholerae

Amphitrichous: one flagellum at each pole e.g. Alkaligens faecalis

Lophotrichous: tuft flagella at one end or both poles e.g. Spirillum

Peritrichous: cell surrounded by lateral flagella. e.g. Salmonella typhi

PILI

Pili (fimbriae): It is hair like structure composed of protein (pilin). Two types (Based on function):

Common pili: The structure for adherence to cell surface.

Sex pili: The structure for transfer of genetic material from the donor to the recipient during the process of conjugation.  

Capsules: this is a layer of loose slimy material which surrounds some bacterial cells. They are protective walls that surrounded the cell membranes of gram positive and gram negative bacteria. Most bacterial capsules consist of polysaccharides but Bacillus anthracis which is unique in that its capsule is made up of amino acids residues

Capsules enable bacteria to be more virulent because macrophages and neutrophils are unable to phagocytize the encapsulated buggers.

Functions

They may provide protection against temporary drying by binding water molecules

They may block attachment of bacteriophages

Promote bacterial attachment to surfaces

They may be antiphagocytic 

BACTERIA WITH DEFECTIVE CELL WALLS:

Bacteria without cell wall can be induced by growth in the presence of antibiotics and a hypertonic environment to prevent lysis. They are of three types:  

Protoplasts: are altered form of bacteria, the term protoplast refers to the spherical shape assumed by Gram-positive bacteria, bounded by a single membrane. Derived from Gram-positive bacteria and totally lacking cell walls; unstable and osmotically fragile; produced artificially by lysozyme and hypertonic medium: 

Spheroplast: refers to the spherical shape assumed by Gram-negative bacteria. It is a sphere that bounded by two membrane. Derived from Gram-negative bacteria; retain some residual but non-functional cell wall material; osmotically fragile; produced by growth with penicillin and must be maintained in hypertonic medium. 

Mycoplasma: refers to a genus of bacteria which lack a cell wall. This characteristic makes them naturally resistant to antibiotics that target cell wall synthesis (like beta-lactam antibiotics).

Characteristics of Mycoplasma       

They are prokaryotic organisms that are surrounded by a triple layered membrane.

They lack true cell wall and resemble L-forms of certain bacteria; they only have cytoplasmic membrane as their outer boundary.

Most Mycoplamas inhabit the mucous membrane of humans or other animals.

Mycoplama may be parasitic, saprophytic or pathogenic.  

They are highly pleomorphic showing small coccoid bodies, ring forms and filamentous forms which may be branched.

L-FORM BACTERIA

Cell wall Deficient Bacteria (CWDB) is also known as L-phase or L-form bacteria

They are bacterial variant that lack a cell wall, although they may in fact possess small amounts of peptidoglycan

The name L-form was given to these bacteria because they were discovered at the Lister Institute London.

L-form bacteria are distinct from Mycoplasma because Mycoplasma spp do not originate from bacteria that normally possess a cell wall. A huge variety of Gram positive and Gram negative bacterial species may become CWDB when exposed to certain stressors in the laboratory (such as antimicrobial drugs)

It exists in 2 forms i.e. (1) Stable L-form: these bacteria remain as CWDB, whereas (2) Unstable L-forms: revert back to possession of a cell wall.

CWDB assume a spherical or pleomorphic shape

BACTERIAL NOMENCLATURE AND TAXONOMIC CLASSIFICATION OF BACTERIA

Classification, nomenclature, and identification are three separate but interrelated areas of bacterial taxonomy.

Classification is the categorization of organisms into taxonomic groups. Classification of bacteria requires experimental and observational techniques; this is because biochemical, physiologic, genetic, and morphologic properties are often necessary for an adequate description of a taxon. 

Nomenclature refers to the naming of an organism by international rules (established by a recognized group of medical professionals) according to its characteristics. 

Identification is practical use of a classification scheme to 

(1) Isolate and distinguish desirable organisms from undesirable ones, 

(2) Verify the authenticity or special properties of a culture in a clinical setting, and

(3) Isolate and identify the causative agent of a disease. 

The latter may lead to the selection of specific pharmacologic treatments directed toward their eradication, a vaccine mitigating their pathology, or a public health measure (e.g., handwashing or use of a condom) that prevents their transmission. Identification schemes are not classification schemes, although there may be some superficial similarity. An identification scheme for a group of organisms can be devised only after that group has first been classified (i.e., recognized as being different from other organisms). For example, the popular literature has reported Escherichia coli as being a cause of hemolytic uremic syndrome (HUS) in infants (is a condition that affects the blood and blood vessels). There are hundreds of different strains that are classified as E coli but only a few that are associated with HUS. These strains can be distinguished from the many other E coli strains by antibody reactivity with their O- and H-antigens. 

Taxonomy, and the nomenclature that accompanies it, is an imprecise and evolving science. Just as our societal vocabulary evolves, so does the vocabulary of medical microbiology. Any professional associated with infectious disease should be aware of the evolving taxonomy of infectious microorganisms.

Domain: highest level constitutes three domains of life

Kingdom: the second most level

Phylum: a group of related classes

Class: a group of related orders

Order: a group of related families

Family: a group of related genera

Genus: a group of related species

Species: a group of similar organisms.

Ranks or Levels of Bacterial

In bacterial taxonomy, a bacterium is placed within a small but homogenous group in a rank or level. Groups of this rank or level unite creating a group of higher rank or level. In bacterial taxonomy, the most commonly used ranks or levels in their ascending order are: species, genera, families, orders, classes, phyla, and domain.

Species is the basic taxonomic group in bacterial taxonomy. Groups of species are then collected into genera (sing, genus). Groups of genera are collected into families (sing, family), families into orders, orders into classes, classes into phyla (sing, phylum), and phyla into domain (the highest rank or level). Groups of bacteria at each rank or level have names with endings or suffixes characteristic to that rank or level.

Rank or level Example

Species E. coli

Genus Escherichia

Family Enterobacteriaceae

Order Enterobacteriales

Class γ-Proteobacteria

Phylum Proteobacteria

Domain Bacteria

Binomial Nomenclature - Organisms are named using binomial nomenclature (viruses are exceptions) - Binomial nomenclature employs the names of the two level taxa, genus and species, to name specie. Binomial nomenclature includes:

Genus 

Genus comes before species (e.g., Escherichia coli) 

Genus name is always capitalized (e.g., Escherichia)

Species name is never capitalized (e.g., coli)

Both names are always either italicized or underlined ( e.g. Escherichia coli )

The genus name may be used alone, but not the species name (i.e. saying or writing “Escherichia “ alone is legitimate while saying or writing “ coli” is not) 

 Strain; A strain is a genetic variant or subtype of a microorganism

Bacterial species – 

A bacterial species is defined by the similarities found among its members. Properties such as biochemical reactions, chemical composition, cellular structures, genetic characteristics, and immunological features are used in defining a bacterial species. Identifying a species and determining its limits presents the most challenging aspects of biological classification for any type of organism.

Methods of Classification 

Phenotypic classification: This is the grouping of microorganisms together based on the mutual similarity of the phenotypic characteristics. This classification system succeeded in bringing order to biological diversity and classified the function of morphological structures. Organisms sharing many characteristics make up a single group or taxon.

Phylogenetic classification: Compares organisms on the basis of evolutionary relationships. The term phylogeny refers to the evolutionary development of species. This method is restricted because of lack of good fossil records.

Genotypic classification: Compares the genetic similarity between organisms’ individual genes or whole genomes can be compared.

Numeric taxonomy: the use of computers. A large number of biochemical, morphological and cultural characteristics is used to determine the degree of similarity between organisms. The advent of computers has made this approach to taxonomy easier to apply. The result of numerical taxonomic analysis is often summarised with a threadlike diagram called a dendogram. 

METHODS OF IDENTIFICATION OF BACTERIA

Bacterial identification methods are tests done to speciate, differentiate or identify bacteria. Most of these tests are based on the biochemical reactions and enzymatic activity of bacteria.