Introduction to Microbiology

• The organisms that cause infectious diseases can be classified as:

  • parasites (protozoa and helminths)
  • fungi
  • bacteria
  • viruses
  • and prions

  Each group has distinctive characteristics with determine how the organisms interact with their hosts and how they cause disease. These characteristics are:

  • structure & molecular make-up
  • biochemical and metabolic strategies to obtain energy and nutrients
  • reproductive processes
• • Bacteria, fungi, and parasites are cellular organisms. Viruses are acellular.
  • Bacteria, fungi, and parasites all possess DNA and RNA. Viruses however only possess either DNA or RNA.
  • Fungi and parasites are eukaryotes. Bacteria is a prokaryote, and viruses are neither prokaryotes or eukaryotes.
  • Fungi and parasites possess 80S ribosomes, bacteria possess 70S ribosomes, and viruses don't have ribosomes.
  • Fungi and parasites possess membrane-bound organelles. Bacteria viruses on the other hand, don't possess membrane-bound organelles.
• • The outer surface of parasites is a flexible membrane
  • the outer surface of fungi is a rigid cell wall containing chitin
  • the outer surface of bacteria is a rigid cell wall containing peptidoglycan.
  • the outer surface of viruses is a protein capsid with a positive or negative lipoprotein envelope.
• • parasites replicate by mitosis
  • fungi replicate by mitosis or budding
  • bacteria replicate by binary fission
  • viruses replicate by using the protein synthesis mechanism of its host cell.
• Macroparasites are large enough to be seen with the naked eye, while microparasites can only bee seen under a microscope.
• The main difference between macroparasites and microparasites is whether they replicate inside the host or not. Microparasites can multiple to produce very large numbers of progeny within the host, thereby causes in overwhelming infection. In contrast, macroparasites don't multiply as quickly, and once the infectious stage has been reached, they mature into the reproductive stage. For macroparasites, replication is via eggs or larvae that then leave the host.
• The level of infection depends on the number of organisms that enter the body. This distinction is important because it influences ecology and epidemiology of parasitic infections.
• Hosts usually develop an immunity to microparasitic infections, but they don't develop an immunity to macroparasitic infections.
• The boundary between macroparasites and microparasites isn't always clear because the progeny of some macroparasites remain within the host and infection can lead to large number of organisms.
• Correct treatment of an infectious disease requires the correct identification of the agent causing it. Taxonomy is the science concerned with the systematic classification of organisms. The systematic division of organisms into related groups is based on similar characteristics shared by all members of the group.
• All pathogens, except for viruses, are named according to the binomial Linnean system. Viruses tend to have a single name.
• Bacteria are very diverse and may be classified using many different properties. Gram stain and bacterial morphology are the two main characteristics commonly used, and a large proportion of clinically important bacteria are classified as either Gram positive or Gram negative based on different staining properties.
• Gram positive and Gram negative bacteria (differentiated based on staining properties) can then be subdivided based on their morphology. Morphological characteristics include nature of the cell wall, shape, and whether they can form spores.
• Bacteria exhibit 1 of 3 basic shapes:

  • they're called bacilli if they're straight and rod-shaped
  • they're called cocci if they're spherical
  • they're called spirilla if they're long and helical

  Some bacilli and cocci form colonies, adhering end-to-end after they've divided to form chains.

  Some bacterial colonies change into stalked structures, growing long branched filaments, or form erect structures that release spores.
• DNA sequencing is useful in determining the evolution of microorganisms by comparing the genomes of different species that can't be grown in vitro.
• Viruses are classified based on the properties of their genome. Such properties include:

  • the type of nucleic acid (DNA or RNA)
  • the number of strands of nucleic acid (ss/ds) and their physical construction
  • polarity of the viral genome (whether the strand of nucleic acid is positive or negative)
  • whether there is a lipid envelope present or not.
• Cells can be prokaryotic or eukaryotic depending on whether there is a distinct nucleus and membrane-bound organelles present or not. Bacteria are the only prokaryotic microbes, whereas fungi and parasites are eukaryotic.
• Helminths are multicellular worms that infest many organs in the body, most commonly the GI tract. They have complex life cycles that progress from egg to larvae to adult.

  Transmission of helminths might be:

  • directly through swallowing infective stages, or by larvae penetrating the skin
  • or indirectly via intermediate non-human hosts.

  The most serious helminth infections are caused by tapeworms and flukes.
• Protozoa:

  • they're unicellular organisms
  • their life cycles include a metabolically active growth stage (trophozoite) and a dormant stage (cyst)
  • many are free-living, or the life cycles may require one or more hosts.
  • protozoa infections are acquired through ingestion of contaminated water or food, or via insect vectors
• Examples of common diseases caused by protozoa are:

  • malaria
  • toxoplasmosis
  • and leishmaniasis
• Most protozoa have enormous reproductive potential because they have short generation times, undergo rapid segmental development, and produce large numbers of progeny. This characteristic is responsible for many acute disease syndromes.
• Fungi:

  • they can grow as single cells (yeasts), branched filaments (hyphae), or both (these have a dimorphic structure). In filamentous fungi, the mass of hyphae forms a mycelium.
  • they have a thick cell wall composes primarily of chitin. This means that fungi aren't sensitive to antimicrobials, such as penicillin, which interferes with peptidoglycan synthesis.
  • species that cause disease may be acquired from the environment, or occur as part of the normal flora.
• Common fungal disease can be superficial in cutaneous and subcutaneous tissue, or in deep tissue. These diseases more most serious in immunocompromised individuals.
• Bacteria are small, unicellular organisms without a nucleus or membrane-bound organelles.

  Essential components of bacteria include:

  • a cell wall - mainly composes of peptidoglycan, and is key for the cell's shape, metabolism, virulence, and antigenicity.
  • a plasma membrane - a phospholipid bilayer
  • 70S ribosomes
  • nucleoid - the area of the cytoplasm in which the genomic DNA is located

  Non-essential components of bacteria include:

  • capsule
  • flagella
  • pili
  • plasmids
  • spores - can allow bacteria to survive in adverse growth conditions
• The cell wall of the bacterium is a multi-layered structure outside the plasma membrane. It's mainly composed of peptidoglycan (also known as murein), which is a monomer consisting of hexose sugars (glycan chain) and amino acids (tetrapeptide chain).

  The sugar component consists alternating residues of N-acetylglucosamine and N-acetylmuramic acid.
• The cell wall is an essential component of bacteria, and is so unique that it can be used to classify them. Bacteria stain differently because of the differences between cell walls.

  The peptidoglycan layer in Gram-positive bacteria is much thicker than in Gram-negative bacteria. Because of the thin peptidoglycan layer, Gram-negative bacteria don't retain the primary staining, and become pink with the safranin counterstain.
• Another difference between Gram-positive and Gram-negative bacteria is that in Gram-negative bacteria, the peptidoglycan layer is overlaid by an outer membrane, which is anchored to the peptidoglycan layer by lipoprotein molecules.

  The outer membrane of Gram-negative bacteria is also rich in lipids and contain lipopolysaccharides (LPS, or endotoxins).
• • Gram-positive bacteria has a thick and multilayers peptidoglycan layer, whereas Gram-negative bacteria have a thin single layer of peptidoglycan.
  • Gram-positive bacteria doesn't possess an outer membrane, nor any lipopolysaccharides. Gram-negative bacteria possess an outer membrane above its peptidoglycan layer, as well as lipopolysaccharides.
  • Gram-positive bacteria have a low lipid and lipoprotein content, whereas Gram-negative bacteria have a high lipid and lipoprotein content.
• Gram-positive bacteria doesn't contain porins - which are protein channels within the membrane that facilitate transport of charged molecules across the outer membrane - whereas Gram-negative bacteria do possess porins.
• Some bacteria have an unusual cell wall that can't be seen under the Gram-stain. This is because they have an outer thick layer of complex, waxy lipids, such as mycolic acids, and the dyes used in the gram-stain won't penetrate this cell wall. Bacteria with this unusual cell wall include mycobacteria, and these are said to be 'acid-fast' because they resist decolorization with acid-alcohol after being stained.
• The Ziehl-Neelsen (ZN) stain is a technique used to stain acid-fast bacteria. When this stain is applied, the mycobacteria are stained bright red.
• The capsule is a non-essential component of a bacterium:

  • it's a gelatinous layer outside the cell wall, mainly composed of polysaccharides. These sugars vary from one species to another.
  • protects the bacterium against the immune system of the host, stopping phagocytes from engulfing the bacteria
  • helps bacteria to adhere to human tissue (the first step in pathogenesis). Hence, bacteria with a capsule are more virulent.
  • Capsules are antigenic; they can elicit the production of antibodies (this property is used for the generation of vaccines).
• Capsules are seen under the microscope when incubated with serum-containing antibodies against the capsule sugars. This is due to the swelling reaction triggered by the binding of the antibodies with the capsule. This makes the capsule opaque and enlarged.
• Flagella is a non-essential component of bacteria that some have:

  • they're long appendages that move the bacteria towards nutrients and other attractants.
  • Flagellated bacteria have a characteristic number and location of flagella: some have one flagellum, others have many. In some, the flagella are located at one end, and in others, they're all over the outer surface.
• Flagella are medically important because:

  • some specifics of motile bacteria are a common cause of urinary tract infections. Flagella play a role in the pathogenesis of these bacteria, as they help propel the bacteria up the urethra into the bladder.
  • Flagella can be used for diagnosis by using specific antibodies against the flagella.
• Pili are a non-essential component of bacteria:

  • they're hair-like filaments that extend from the cell surface
  • mainly found on Gram-negative organisms
  • they're thinner and shorter than flagella
• Pili have 2 main functions:

  • They allow bacteria to attach to specific receptors on the host's cell surface.
  • A specialised type of pili, called a sex pili, form the necessary bridge-like connection between bacteria during conjugation - a mechanism employed by bacteria to exchange genetic material.
• Plasmids are extrachromosomal, double-stranded, circular DNA molecules that are capable of replicating independently of bacterial chromosome.

  • they exist in both Gram-positive and Gram-negative bacteria
  • they can encode for useful characteristics, such as antibiotic resistance, resistance to heavy metals present in some antiseptic substances, and toxic production.
  • plasmids can be transmitted from one bacterium to another by 3 mechanisms: conjugation, transduction, and transformation.
• Spores:

  • formed in response to adverse conditions by some medically-important, Gram-positive bacteria.
  • never formed by actively growing cells, so they're not usually seen in specimens recovered from patients infected with spore-forming bacteria.
  • contain bacterial DNA surrounded by a thick keratin-like coat that confers resistance to heat, chemicals, or drying.
• Spore formation is known as sporulation, and it occurs when nutrients are depleted from the environment. Spores allow the bacteria to survive until the conditions become favourable again. Once favourable conditions have arrives, the spore germinates into a new bacterial cell.