Chapter 2 Medical Microbiology

Bacteria Definition

“Bacteria are unicellular organisms belonging to the prokaryotic group where the organisms lack a few organelles and a true nucleus”.

Bacteria Diagram

The image below represents the structure of a typical bacterial cell with its different parts. 

• Cell Wall

• Plasmid

• Cytoplasm

• Flagella

Ultrastructure of a Bacteria Cell

The structure of bacteria is known for its simple body design. Bacteria are single-celled microorganisms with the absence of the nucleus and other cell organelles; hence, they are classified as prokaryotic organisms.

They are also very versatile organisms, surviving in extremely inhospitable conditions. Such organisms are called extremophiles. Extremophiles are further categorized into various types based on the types of environments they inhabit:

1. Thermophiles

2. Acidophiles

3. Alkaliphiles

4. Osmophiles

5. Barophiles

6. Cryophiles

Another feature of bacteria is their protective cell wall, which is made up of a special protein called peptidoglycan. The components of bacterial cell wall forms an important basis upon which the bacteria can be divided. This particular protein isn’t found anywhere else in nature except in the cell walls of bacteria.

But few of them are devoid of this cell wall, and others have a third protection layer called capsule. On the outer layer, one or more flagella or pili is attached, and it functions as a locomotory organ. Pili can also help certain bacteria to attach themselves to the host’s cells. They do not contain any cell organelle as in animal or plant cell except for ribosomes.

Ribosomes are the sites of protein synthesis. In addition to this DNA, they have an extra circular DNA called plasmid. These plasmids make some strains of bacteria resistant to antibiotics.

Classification of Bacteria

Bacteria can be classified into various categories based on their features and characteristics. The classification of bacteria is mainly based on the following:

• Shape

• Composition of the cell wall

• Mode of respiration
  

• Mode of nutrition

Classification of bacteria based on Shape

Classification of bacteria based on the Composition of the Cell Wall

Classification of bacteria based on the Mode of Nutrition

Classification of bacteria based on the Mode of Respiration

Reproduction in Bacteria

Bacteria follow an asexual mode of reproduction, called binary fission. A single bacterium divides into two daughter cells. These are identical to the parent cell as well as to each other. Replication of DNA within the parent bacterium marks the beginning of the fission. Eventually, cell elongates to form two daughter cells.

What is a Virus?

Viruses are non-cellular, microscopic infectious agents that can only replicate inside a host cell. From a biological perspective, viruses cannot be classified either a living organism or non-living. A virus can be an infectious agent which only replicates within a host organism. This is due to the fact that they possess certain defining characteristic features of living organisms and non-living entities.

In a nutshell, a virus is a non-cellular, infectious entity made up of genetic material and protein that can invade and reproduce only within the living cells of bacteria, plants and animals.

For instance, a virus cannot replicate itself outside the host cell. This is because viruses lack the required cellular machinery. Therefore, it enters and attaches itself to a specific host cell, injects its genetic material, reproduces by using the host genetic material and finally the host cell splits open, releasing the new viruses.

Viruses can also be crystallized, which no other living organisms can do. It is these factors that lead to viruses being classified in the grey area – between the living and non-living.

Structure and Function of Viruses

Viruses are tiny and smaller in its size, ranging between 30-50 nm. Viruses do not contain cells and usually lack a cell wall but are surrounded by a protective protein coating called the capsid. It can be seen as a genetic element and is characterized by the combined evolution of the virus and the host. They contain either RNA or DNA as the genetic material.

Viruses mainly depend on a host to deliver the complex metabolic machinery of prokaryotic or eukaryotic cells for propagation. The main task of the virus is to carry its DNA or RNA genome to the host cell, which then can be transcribed by the host cell. The viral genome structure is packed in a capsulated symmetric protein. The protein associated with nucleic acid (also known as nucleoprotein) produces the nucleocapsid with the genome.

Classification of Viruses

Viruses can be classified primarily on their phenotypic characteristics, core content, chemical composition, capsid structure, size, shape, modes of replication and other viral genome structures.

Classification based on the presence of nucleic acid

DNA virus

The virus, having DNA as its genetic material. There are two different types of DNA virus

Single-stranded (ss) DNA virus: e.g. Picornaviruses, Parvovirus,  etc.

Double-stranded (ds) DNA virus: e.g. Adenovirus, Herpes virus, etc.

RNA virus

The virus, having RNA as its genetic material. There are two different types of RNA virus

Double-stranded (ds) RNA virus: e.g. Reovirus, etc.

Single-stranded (ss) RNA virus. It is further classified into two Positive sense RNA (+RNA) and negative sense RNA (-RNA). Poliovirus, Hepatitis A, Rabies virus, Influenza virus are examples of single-stranded RNA virus.

Classification based on the structure or symmetry

Viruses come in different shapes, from basic helical and icosahedral shapes to more intricate ones. The classification based on different shapes and symmetry of viruses are as follows:

1. Complex virus. E.g Poxvirus

2. Radial symmetry virus. E.g.Bacteriophage

3. Cubical or icosahedral symmetry shaped virus. E.g. Reovirus, Picornavirus

4. Rod or Spiral shaped or helical symmetry virus. E.g. Paramyxovirus, orthomyxovirus

Classification based on the replication properties and site of replication

Here, viruses invade into the host cell, where it replicates and assembly within the cell organelles.

1. Replication within the cytoplasm of the host cell.
   E.g. All RNA viruses except the Influenza virus.

2. Replication within the nucleus and the cytoplasm of the host cell.
   E.g. Influenza virus, Poxvirus, etc.

3. Replication within the nucleus of the host cell.
   All DNA viruses except Pox virus.

4. Replication of the virus through the double-stranded DNA intermediate.
   E.g. All DNA viruses, Retrovirus and some tumour causing RNA virus.

5. Replication of the virus through a single-stranded RNA intermediate.
   E.g. All RNA viruses except Reovirus and tumour-causing RNA viruses.

Classification based on the host range

Based on the type of host, there are four different types of viruses:

Animal viruses

These viruses infect by invading the cells of animals, including humans. Prominent examples of animal viruses include the influenza virus, mumps virus, rabies virus, poliovirus,  Herpes virus, etc.

Plant viruses

These viruses infect plants by invading the plant cells. Replication of plant viruses is obligate and does not happen without a host. Well-known examples of plant virus include the potato virus, tobacco mosaic virus (TMV), beet yellow virus, and turnip yellow virus, cauliflower mosaic virus, etc.

Bacteriophage

The virus which infects bacterial cells is known as bacteriophage. There are many varieties of bacteriophages, such as DNA virus,  MV-11, RNA virus, λ page, etc.

Insect virus

The virus which infects insects is known as Insect virus, also called the viral pathogen of insects. These viruses are considered as a powerful biocontrol agent in the landscape of modern agriculture. Ascovirus virions and  Entomopox virus, are best examples for insect virus.

Classification based on the mode of transmission

1. Airborne infections – Transmission of the virus through the air into the respiratory tract. E.g. Swine flu, and Rhinovirus.

2. Fecal oral route  – Transmission of the virus through the contaminated water or food.
   E.g. Hepatitis A virus, Poliovirus, Rotavirus.

3. Sexually transmitted diseases – Transmission of the virus through sexual contacts with the infected person. E.g. Retrovirus, human papillomavirus, etc.

4. Transfusion-transmitted infections- Transmission of the virus through the blood transfusion.
   E.g. Hepatitis B virus, Human Immunodeficiency Virus, etc.

5. Zoonoses -Transmission of the virus through the biting of infected animals, birds, and insects to human. E.g. Rabies virus, Alpha virus, Flavivirus, Ebola virus, etc.

Virus Reproduction

Lytic infection is the method used by the majority of viruses to reproduce. A virus penetrates the host cell during lytic infection, replicates, and causes the cell to lyse or explode.

Overview of the lytic cycle:

• Attachment: Virus binds to host cell during attachment.

• Entry: Injection of genetic material into the host cell.

• Replication: The virus takes control of the host cell’s metabolism, leading the organelles to produce new proteins and nucleic acids.

• Assembly: Nucleic acids and proteins are put together to form new viruses during assembly.

• Release: Viral enzymes induce the host cell to burst, releasing viruses into the surrounding environment. These novel viruses are capable of infecting other cells.

List of Viral Diseases

Following is a list of virus diseases that have made a significant socioeconomic impact in the last few decades.

• AIDS (Acquired Immunodeficiency Syndrome)

• Ebola

• Influenza

• SARS (Severe Acute Respiratory Syndrome)

• Chikungunya

• Small Pox (Now eradicated)

Economic Importance of Virus

Viruses are used in biotechnology research because they share the properties of living and non-living species. The viruses can be both helpful and harmful. Bacteriophage can be used to preserve water since it can eliminate germs and maintain the freshness of the liquid.

• Pox, polio, mumps, jaundice, and other diseases can be controlled by injecting dead viruses into people as vaccines, which is how antidotes and vaccines are made.

• A specific virus can control some insects and animals that are hazardous to people.

• Disease management: The T2 bacteriophage virus protects from dysentery by killing dangerous bacteria, such as E-coli. Because viruses can specifically target cells and DNA, they are used in virotherapy to treat various disorders. It might play an essential role in gene therapy and cancer treatment.

• The most familiar living model utilised in laboratories is the virus. In genetics research, viruses are primarily used. It is an essential topic of discussion in genetic engineering.

• Due to the virus’s combination of living and non-living traits, it is necessary to understand the evolutionary tendency and the mechanism by which living entities are created.

• Viruses are an example of an organic nanoparticle in nanotechnology. They have been utilised as a model for arranging materials on the nanoscale due to their shape, size, and structures.

• One million viruses can be found in a spoonful of seawater, aquatic ecosystems’ most abundant natural component. A virus can boost the number of photosynthesis in oceans and reduce the quantity of carbon dioxide in the atmosphere by about three gigatonnes of carbon per year.

What is Fungi?

Fungi are eukaryotic organisms that include microorganisms such as yeasts, moulds and mushrooms. These organisms are classified under kingdom fungi.

Structure of Fungi

The structure of fungi 

• Almost all the fungi have a filamentous structure except the yeast cells.

• Can be either single-celled or multicellular organisms.

• Fungi consist of long thread-like structures known as hyphae. These hyphae together form a mesh-like structure called mycelium.

• Fungi possess a cell wall which is made up of chitin and polysaccharides.

• The cell wall comprises a protoplast, which is differentiated into other cell parts such as cell membrane, cytoplasm, cell organelles and nuclei.

• The nucleus is dense, clear, with chromatin threads. The nucleus is surrounded by a nuclear membrane.

Characteristics of Fungi

• Fungi are eukaryotic, non-vascular, non-motile and heterotrophic organisms.

• They may be unicellular or filamentous.

• They reproduce by means of spores.

• Fungi exhibit the phenomenon of alternation of generation.

• Fungi lack chlorophyll and hence cannot perform photosynthesis.

• Fungi store their food in the form of starch.

• Biosynthesis of chitin occurs in fungi.

• The nuclei of the fungi are very small.

• The fungi have no embryonic stage. They develop from the spores.

• The mode of reproduction is sexual or asexual.

• Some fungi are parasitic and can infect the host.

• Fungi produce a chemical called pheromone leading to sexual reproduction in fungi.

• Examples include mushrooms, moulds and yeast.

Classification of Fungi

Based on Mode of nutrition

On the basis of nutrition, kingdom fungi can be classified into 3  groups.

Saprophytic – The fungi obtain their nutrition by feeding on dead organic substances. Examples: Rhizopus, Penicillium and Aspergillus.

Parasitic – The fungi obtain their nutrition by living on other living organisms (plants or animals) and absorb nutrients from their host. Examples: Taphrina and Puccinia.

Symbiotic – These fungi live by having an interdependent relationship with other species in which both are mutually benefited. Examples: Lichens and mycorrhiza. 

Based on Spore Formation

Kingdom Fungi are classified into the following based on the formation of spores:

Zygomycetes – These are formed by the fusion of two different cells. The sexual spores are known as zygospores, while the asexual spores are known as sporangiospores. Example – Mucor.

Ascomycetes – Also called sac fungi. Can be coprophilous, decomposers, parasitic or saprophytic. The sexual spores are called ascospores. Asexual reproduction occurs by conidiospores. Example – Saccharomyces.

Basidiomycetes – Mushrooms are the most commonly found basidiomycetes and mostly live as parasites. Sexual reproduction occurs by basidiospores. Asexual reproduction occurs by conidia, budding or fragmentation. Example- Agaricus.

Deuteromycetes – Otherwise called imperfect fungi as they do not follow the regular reproduction cycle as the other fungi. They do not reproduce sexually. Asexual reproduction occurs by conidia. Example – Trichoderma.

Reproduction in Fungi

Examples of Fungi

• Yeast

• Mushrooms

• Moulds

• Truffles