A pathogen is something of biological origin that causes disease in a host and may include:

  • Non-living agents - such as viruses and prions
  • Living microorganisms - such as bacteria, fungi and eukaryotic parasites (typically protozoa, platyhelminthes and arthropods)


  • Viruses are metabolically inert and incapable of reproducing independently of a host cell (hence are not living)
  • Structurally, viruses consist of an inner core of nucleic acid surrounded by a protein coat (capsid)
    • Simpler viruses may lack a capsid (viriods), while more complex viruses may contain an external lipid envelope
  • Viruses can either be DNA-based (adenoviruses) or RNA-based (retroviruses) 
    • Retroviruses require a special enzyme (reverse transcriptase) to convert its RNA into DNA form
  • Viruses may either commandeer the host machinery to replicate independently of the host genome (lytic cycle) or integrate into the host genome and be reproduced while dormant in cell progeny (lysogenic cycle)
  • In both cases, the virus will eventually replicate itself thousands of times, before lysing the cell and releasing its infectious copies (virions)
  • Examples of adenoviruses include the rhinovirus (common cold) and herpes simplex virus (herpes and cold sores)
  • An examples of a retrovirus is the human immunodeficiency virus - or HIV (responsible for AIDS)
  • Viruses which infect bacteria are known as bacteriophages

Stages of Viral Replication


  • A prion (proteinaceous infectious particle) is a protein that has refolded abnormally into a structure that is capable of causing disease
  • It is also able to convert normally folded protein molecules into the abnormal form (mechanism of conversion not well understood)
  • Infectious prion proteins have a higher content of beta-pleated sheets, which increases structural stability making them more resistant to denaturation
  • This makes treatment of prion proteins extremely difficult (there are currently no known cures)
  • Prion proteins aggregate together to form amyloid fibrils capable of causing disease
  • Diseases caused by prion proteins are called spongiform encephalopathies, because they cause holes to form within the brain
  • Examples of prion diseases include:
    • Mad cow disease (affects cows)
    • Scrapie (affects sheep)
    • Creutzfeld-Jacob disorder (CJD) and kuru (affects humans)

Folding and Replication of Prion Protein


  • Bacteria are unicellular prokaryotes and may be classified according to a number of different features, including:
    • Shape (spherical = coccus ; rod = bacillus ; spiral = spirella / vibrio / spirochete)
    • Associative patterns (pairs = diplo ; chains = strepto ; bunches = staphylo)
    • Cell wall composition (Gram positive versus Gram negative)
    • Gaseous requirements (aerobe, facultative anaerobe, obligate anaerobe) 
  • Most bacteria are relatively harmless to humans and may even form a beneficial mutualistic relationship (e.g. normal flora in the digestive tract)
  • Harmful bacteria may cause disease by competing with beneficial bacteria and local cells for space and resources (e.g. nutrients)
  • Bacteria may also cause disease by releasing poisonous substances called toxins
    • Exotoxins are secreted into the surrounding environment by bacteria
    • Endotoxins are internal components of a bacteria that become toxic when the bacteria cell is destroyed
  • As toxins retain their destructive capabilities after the death of the bacterium, they are often the cause of food poisoning (when food is heated sufficiently to destroy the bacteria but not the toxin)

Exotoxins versus Endotoxins


  • Fungi are important decomposers in biological systems
  • They can be categorised according to whether they are unicellular (yeasts) or multicellular (moulds) - the majority of fungi are moulds
  • Fungi usually attack the body surfaces, including skin and mucous membranes
  • The moulds consist of branching filaments called hyphae, which may form a mass of invading threads called mycelium
  • Examples of fungal infections include:
    • Yeast - Thrush (irritation of the mouth and vagina caused by the genus Candida)
    • Moulds - Athlete's foot (irritation of the feet and finger webbing caused by the genus Tinea)

Hyphal Filaments of a Fungus


  • A parasite is an organism that grows, feeds and is sheltered on or in a different organism, while contributing nothing to the survival of the host
  • A parasite benefits at the expense of the host organism
  • Parasites can be defined as either ectoparasites (living on the surface of the host) or endoparasites (living within the host)


  • Ectoparasites are commonly arthropods (insects, spiders, etc.) and may cause disease in humans either directly or indirectly
  • Arthropods such as lice, ticks and mites feed on the blood and may directly cause disease by injecting substances that act as toxins
  • Insects such as fleas and mosquitoes may not have an inherently harmful bite but may indirectly cause disease by acting as a vector
  • A vector is an organism that transmits a pathogen from a source to a host
  • There are two types of vectors:
    • Biological vectors accommodate the disease-causing microorganism while it undergoes part of its life cycle (e.g. the malarial mosquito)
    • Mechanical vectors are not involved in the growth and development of the microorganism and simply carry it from a source to a host


  • Endoparasites live within the host and include microparasites (e.g. small, single-celled protozoa) or macroparasites (e.g. multicellular helminths)
    • Examples of protozoa which cause disease include Plasmodia (responsible for malaria) and Trypanosoma (African sleeping sickness)
    • Examples of helminth which cause disease include roundworm, tapeworm and flatworm (note: 'ringworm' is a fungal infection)

Transmission of Malaria  (Life Cycle of Plasmodium)