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Pathogenic microorganisms

Communicable disease

Communicable disease spreads from affected individuals to those unaffected. Pathogens are microorganisms which can cause disease. These include bacteria, viruses and fungi. Have a look at the little things!


Pathogens can cause disease when they invade the interface between an organism and their environment. This could be someone's skin, lungs, digestive system, etc.

There are multiple ways in which pathogens cause disease. Bacteria can produce toxins, viruses take over cellular machinery such as enzymes and nutrients and destroy the cells in the process, while fungi can secrete enzymes that break down host tissue.

There are many different kinds of bacterial toxin e.g. by Staph. aureus, such as protein barrels that integrate into the plasma membrane of host cells and cause their contents to leak out through these huge pores created by the barrel shape.



Viruses are tiny microscopic entities that have absolutely no activity whatsoever. In the presence of a larger organism of their specific fit (and there are viruses to target anything), they come alive by hijacking its life tools: nutrients, energy, ribosomes, you name it.

They only carry the genetic information they need to invade and replicate. Invade and replicate. A bit of a glitch of life, or the perfect expression of it?



Both DNA and RNA viruses make use of their host's transcription and translation machinery such as ribosomes and enzymes to enable protein synthesis. Retroviruses on the other hand bring their own reverse transcriptase enzyme to enable the production of DNA using their RNA template once inside the host cell. Once the RNA is reverse transcribed into DNA (DNA->RNA is transcription, hence RNA->DNA is reverse transcription), the normal protein synthesis pathway can take place.

Not only does the viruses invade, replicate and kill the host cell, making it burst (lyse), but it can invade and just lie quietly inside the host cell's genetic material until a later time.

Fungi such as those causing athlete's foot secrete enzymes that break down keratin in the skin, causing the associated symptoms.


Tuberculosis (TB)

Tuberculosis (TB) is an infectious disease of the lungs which causes constant coughing with blood, shortness of breath, fever and weight loss over the years. Every year 2 million people die from TB out of 8/10 million who get the disease. Far more people, around 2 billion, carry the TB bacteria on them without having the disease. This is primary TB.

TB is passed on between people by inhaling droplets from the air infected with the bacteria Mycobacterium tuberculosis. When the infection is confirmed, patients are isolated for up to 4 weeks and put on a course of antibiotics for up to 6 months. This is secondary TB as the dormant bacteria that have accumulated in the lymph nodes during the symptom-free primary TB stage now escape and start causing symptoms and damage to the lungs.




When bacteria reach the alveoli, the immune system reacts by surrounding them with white blood cells, which results in the formation of scar tissue. The shortness of breath symptom is caused by less oxygen reaching the circulatory system due to a decreased surface area for diffusion in the lungs, as many alveoli are damaged.

Treatment involves a course of antibiotics which can be lengthy, resulting in many patients stopping at the first signs of amelioration of their symptoms. This causes resistance in the bacteria, which come back to cause disease. Moreover, antibiotic-resistant strains have emerged. There are multi-drug resistant strains which are not affected by the main antibiotics (isoniazid and rifampicin), and even totally drug resistant TB. Managing antibiotic use is crucial to preventing resistance. This includes keeping some antibiotic types as a backup by not using them at all (last resort drugs).

There is a vaccine that protects partially against TB and is administered to children, slightly reducing their probability of contracting the infection, as well as substantially reducing the probability that if they get infected it will cause the disease symptoms. Other prevention strategies include isolating symptomatic patients, and solving crowding problems in households, as prolonged contact between carriers can contribute to the spread of the infection to susceptible people.


Acquired immune deficiency syndrome (AIDS)

The human immunodeficiency virus (HIV) causes acquired immune deficiency syndrome (AIDS). Upon infection, it replicates in helper T cells. HIV is a lentivirus with the expected viral components such as its genetic material (RNA in this case) and capsid.
Upon infection via transmission of infected bodily fluids such as blood or semen (opportunistic infection), the virus seeks its host cell, the helper T cell which is a key component of the immune response. As HIV hijacks the cell's machinery to replicate, it destroys it and thus impedes the immune response, leaving the victim with a compromised immunity and therefore susceptible to opportunistic infections.

Part of the HIV replication strategy is the embedding of its genetic material into the host cell's DNA. The virus contains RNA which has to first be converted into DNA. This is what the reverse transcriptase enzyme does (transcription is DNA to RNA, so reverse transcription is RNA to DNA).

Some drugs for AIDS take advantage of this DNA embedding step by preventing it, and therefore slowing down the replication process of the virus. The reason antibiotics don't work on any viruses is quite simple. We've seen that prokaryotes like bacteria are a cell of their own with many different structures and organelles such as a cell wall, while viruses are neither a cell nor alive. You can imagine you can't really target something as vague as a piece of genetic information in a protein capsid.

Bacteria have complex cell walls with many components and various enzymes building them up or performing other metabolic functions within the cell. Any of these parts or processes can be targeted, as long as it is distinct from its host (that is ourselves with our eukaryotic cells that do not, for example, have cell walls and thus won't be harmed by the antibiotic if that's the part it targets). Viruses have no cell walls, no ribosomes, nothing really taking place.


Bacterial identification

The simplest classification system of bacteria is based on their shape and arrangement. Bacteria come in sphererodspiralcomma and filament shapes, and can be paired up in twosstrings or 3D shapes. Using the diagram, can you figure out what Staphylococcus aureusVibrio cholerae and Streptococcus sp. look like?




Gram test

Amongst bacteria, the cell wall composition is a key determinant of what type they belong to. This is important in terms of predicting their response to various antibiotics. Based on different bacteria species' response to crystal violet stain, Gram positive bacteria are able to take up the stain and appear violet under a microscope, while Gram negative bacteria do not take the stain up and will appear pink if a counterstain is added after washing off the crystal violet stain (this will persist in the Gram positive bacteria).




Iodine is added after the stain in order to bind to it and trap it inside the bacteria. Acetone is used in the decolorisation step. Any free stain is washed off. In gram positive bacteria, the stain persists. The difference arises because different bacteria have different cell walls. The bacterial cell wall is one of the main targets of antibiotics.



Notice the difference in thickness of the murein layer in gram positive versus gram negative cells. This layer is what absorbs the violet stain. Hence gram positive bacteria turn violet, while gram negative bacteria lose the stain upon washing.


Incidence and prevalence of disease

Epidemiology is the study of breakouts and spread of infectious diseases.

Where disease is present constantly over time, it is said to be endemic, for example as tuberculosis is endemic to parts of India. When an otherwise absent or infrequent disease surges in cases in a population, it creates an epidemic. If an epidemic spreads internationally, then it becomes a pandemic.

For example, chickenpox is endemic to the UK, SARS (severe acute respiratory syndrome) caused an epidemic in China in 2002, and H1N1 influenza caused a pandemic in 2009.

Tracking these events requires calculating incidence rates, prevalence rates and mortality rates.

The incidence rate of a disease refers to the new cases of infected individuals per population, over a specific time period.




For example, in 2001 there were around 13 cases per 100,000 people (0.013%) in England and Wales. The incidence rate in London, however, was almost triple that with around 37 cases per 100,000 people (0.037%).

The prevalence rate of a disease represents the number of affected individuals per population, over a given time frame. Unlike the incidence rate, the prevalence rate refers to all individuals affected by that disease, not just those that have newly acquired it.


For example, the HIV prevalence rate in Mexico, Brazil, Ireland, Morocco, Iran and Indonesia was < 1% in 2014, while that in South Africa was > 10%, with a global prevalence rate of 0.8%.

The mortality rate is the number of affected individuals in the population that have died in a specific time period.



The mortality rate for tuberculosis in the UK between the 1880's and World War I (WWI) through the 1920's fell sharply from around 230 per 100,000 people (0.23%) to around 130 per 100,000 people (0.13%).

The identification of the TB bacterium and skin testing underpinned this drop. A brief rise in mortality rate was seen during both WWI and WWII, followed by further drops.


Control and prevention

Part of controlling and preventing communicable disease in the UK is the legal duty to report notifiable diseases. For example, a GP has to inform the local authority whenever a case of a notifiable disease (that must be monitored to prevent spread and contain an emerging epidemic) occurs.

There are around 30 notifiable diseases including leprosy, plague, tuberculosis, food poisoning, anthrax, cholera, malaria, whooping cough and dysentery.

Public Health England is a government agency responsible for the good health and wellbeing of the public. It monitors trends in public health, so any unusual events such as sudden increased deaths of a particular cause serve to predict and inform impeding epidemics.

Attempts to control and prevent diseases such as AIDS and TB are subject to social, ethical, economic and biological factors.

Social factors refer to how people interact with each other. HIV can be transmitted sexually and relies on timely diagnosis and information. How people approach getting tested for HIV, as well as disclosing if they are HIV positive to sexual partners are factors involved in the control and prevention of infections. Disclosure is also an ethical matter.




TB involves committing to long courses of antibiotics, and is transmitted in crowded environments. Compliance, caring responsibilities and socio-economic status are all factors that affect the control and prevention of infection.

Biological factors determine the parameters within which communicable disease operates. For example, the TB bacterium takes a long time to grow in the lab, leading to long waiting times for conclusive diagnosis. This means that treatment must begin before definitive diagnosis is given. TB symptoms also improve partway through treatment, leading patients to abandon their course of treatment.

Both HIV and Mycobacterium tuberculosis settle in the body long-term, if not permanently. This complicates the control and prevention of infections, as patients become and remain carriers, going through patent and active periods of illness.

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