APPLIED MICROBIOLOGY AND PARASITOLOGY (MB-EN 200)

CERTIFICATE IN ENROLLED NURSE AND MIDWIFE/ ACCOUCHEUR

STUDENT HANDBOOK

(2023)

Student name ………………………………………………..……

Intake: ………………………………………………………….…
TABLE OF CONTENTS

UNIT 1: GENERAL MICROBIOLOGY .......................................................................................... 4

1.1. INTRODUCTION TO MICROBIOLOGY ........................................................................... 4
1.2. STERILIZATION AND DISINFECTION............................................................................. 8
1.3. HOSPITAL WASTE MANAGEMENT ............................................................................... 14
1.4. INFECTIONS.......................................................................................................................... 17
1.5. NORMAL MICROBIAL FLORA ........................................................................................ 21
UNIT 2: IMMUNOLOGY ................................................................................................................ 23
2.1. IMMUNITY, ANTIGEN (AG), IMMUNOGLOBULIN’S(IGS) – ANTIBODIES (ABS)23
2.2. IMMUNE SYSTEM................................................................................................................ 26
2.3. IMMUNE RESPONSE ........................................................................................................... 29
2.4. HYPERSENSITIVITY ........................................................................................................... 31
2.5. IMMUNIZATION AND IMMUNIZATION SCHEDULE ................................................ 32
UNIT 3: BACTERIOLOGY ............................................................................................................. 36
UNIT 4: MYCOBACTERIA ............................................................................................................ 42
UNIT 5: VIROLOGY ........................................................................................................................ 45
UNIT 6: MYCOLOGY ..................................................................................................................... 49
UNIT 7: PARASITOLOGY ............................................................................................................. 51
UNIT 8: CLINICAL MICROBIOLOGY........................................................................................ 56
8.1 SEPTICEMIA AND BACTEREMIA .................................................................................... 56
8.2. PYREXIA OF UNKNOWN ORIGIN (PUO) ....................................................................... 56
8.3. MENINGITIS.......................................................................................................................... 57
8.4. RESPIRATORY TRACT INFECTIONS (RTI) .................................................................. 58
8.5. DIARRHEAL DISEASES ...................................................................................................... 59
8.6. URINARY TRACT INFECTION (UTI) .............................................................................. 60
8.7. SEXUAL TRANSMITTED DISEASES ............................................................................... 61
8.8. HOSPITAL ACQUIRED INFECTION ............................................................................... 62

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ABBREVIATIONS AND ACRONYMS

AB: Antibody

AG: Antigen

HMI: Humoral mediated immunity

CMI: Cell mediated immunity

DNA: Deoxyribonucleic Acid

ECF: Extracellular Fluid

ELISA: Enzyme-linked Immunosorbent Assay

HSV: Herpes Simplex Virus

IG: Immunoglobulin

LTBI: Latent TB Infection

PID: Pelvic inflammatory Disease

PUO: Pyrexia of Unknown Origin

RTI: Respiratory Tract Infections

RES: Reticuloendothelial System

RNA: Ribonucleic Acid

TB: Tuberculosis

UTI: Urinary Tract Infection

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 UNIT 1: GENERAL MICROBIOLOGY
1.1. INTRODUCTION TO MICROBIOLOGY

Objectives
At the end of this chapter, students should be able to:
• Define microbiology
• Group microorganisms based on morphological and functional properties.
• Know to which taxonomic kingdom different microorganisms belong
• Enumerate the differences between prokaryotes and eukaryotes
• Discuss the beneficial and harmful effects of microorganisms on human, animal and plant life.
• Discuss the contribution of scientists to the field of microbiology

Introduction
The earth on which we are living is an excellent place for the existence of different forms of life such
as animals, human beings, plants, which are visible to the naked eye and are called macro-organisms.
In addition, there is existence of other forms of life, which are invisible to the naked eye. These
organisms are called microorganisms (micro = small, bious = life).

Definitions
Microbiology: The science that deals with the study of microorganisms and their activities.

Based on morphological and functional properties, microorganisms are grouped as:

• Bacteria: small, unicellular, microscopic organisms with primitive nucleus.
• Fungi: unicellular or multicellular microscopic organisms with well-developed nucleus. They
possess plant like structure but are devoid of chlorophyll and are not differentiated into roots, stem,
leaves, etc.
• Algae: unicellular or multicellular microscopic organisms possessing plant like characters. They
have chlorophyll but are not differentiated into roots, stems, leaves, flowers, etc. Most of them
possess a well-developed nucleus, except blue green algae.
• Protozoa: unicellular, non-photosynthetic microscopic organisms possessing animal like
characters. Have well developed nucleus

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• Viruses: very small, ultramicroscopic (seen under electron microscope), noncellular
microorganisms capable of multiplying only inside the living cell. They are different from the other
living creatures.

To which taxonomic kingdom do microorganisms belong?

In early history, living organisms were classified into two kingdoms:
• Plant kingdom
• Animal kingdom
Later on, a new kingdom Protista was proposed for microorganisms by Ernest Haeckel (1866). All
bacteria, fungi, Algae and protozoa are grouped in the kingdom Protista. Viruses are not included
because they do not have cellular organization. The kingdom Protista is further divided into two
groups based on structural (cellular organization) differences among the microorganisms as:
• Prokaryotes
• Eukaryotes
Bacteria and blue-green algae are prokaryotes, while fungi, other algae, slime molds and protozoa
are eukaryotes.

The differences between prokaryotes and eukaryotes are presented in the table below:

Prokaryotes Eukaryotes
DNA DNA is naked DNA is bound to protein
DNA is circular DNA is linear
Organelles No nucleus Has a nucleus
No membrane bound organelles Membrane bound organelles
70S ribosomes 80S ribosomes
Reproduction Binary fission Mitosis and meiosis
Single chromosome (haploid) Chromosomes paired (diploid or
more)
Average Size Smaller (Less than 5 µ) Larger (Greater than 5 µ)
Examples Bacteria, blue green algae Algae, Fungi, Protozoa

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Microorganisms are beneficial as well as harmful to human beings, animal and plants.

Beneficial Effects
• Produce organic acids like citric acid, lactic acid, acetic acid, etc.
• Produce vitamins, amino acids, enzymes, etc.
• Produce wines and alcohol
• Fix atmospheric nitrogen into organic matter and thus help to increase the soil fertility.
• Methanogenic bacteria produce methane gas, which is a biofuel.
• Produce antibiotics, which are used for the treatment of infectious disease caused by pathogenic
microorganism.

Harmful Effects
• Cause disease in man, animal and plants.
• Spoil food, water, books, leather and furniture

Pioneers in the science of microbiology

Antony van Leeuwenhoek (1632–1723)
• Constructed the first microscopes
• Demonstrated for the first time the capillary connections between arteries and veins
• Discovered the presence of bacteria and spirochetes in mouth

Edward Jenner (1749–1823)

• Discovered vaccine against small pox which ultimately led to the eradication of small pox
(Variola).

Louis Pasteur (1822–1895)

• Father of microbiology
• Coined the term microbiology for the study of organisms of microscopic size
• He discovered the importance of sterilization and discovered steam sterilizer, autoclave and hot
air oven
• He differentiated between aerobic and anaerobic bacteria
• He developed a live attenuated anthrax vaccine.
• He is a founder of “Germ theory of disease”

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Robert Koch (1843–1912)
• Father of bacteriology
• He discovered bacterium (M. tuberculosis) which cause TB and bacterium (Vibrio cholerae)
which causes cholera
• Well known for ‘Koch’s postulates’

Joseph Lister (1827–1912)

• He is popularly known as “Father of antiseptic surgery”

Alexander Fleming (1881–1955)

• Associated with two major discoveries-lysozyme and penicillin.

Paul Ehrlich (1854–1915)

• Father of Chemotherapy.

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 1.2. STERILIZATION AND DISINFECTION

Objectives
At the end of this chapter, students should be able to:
• Define terms related to Sterilization and Disinfection
• State the factors Influencing the efficacy of a sterilant/ disinfectant
• Classify items to be sterilized or disinfected
• Discuss different Methods of sterilization
• Discuss Methods of disinfection
• List the characteristics of an ideal disinfectant
• Discuss the application of disinfectants

Introduction
Disinfection and sterilization are essential for ensuring that medical and surgical instruments do not
transmit infectious pathogens to patients.

Definitions
Sterilization: Is a process by which an article, surface or medium is made free of all
microorganisms, including their spores.
Disinfection: Describes a process that eliminates many or all pathogenic microorganisms, except
bacterial spores, on in animate objects.
Cleaning: It is the removal of visible soil (e.g., organic and inorganic material) from objects and
surfaces.
Decontamination: The removal of pathogenic microorganisms from objects so they are safe to
handle, use, or discard.
Disinfectant: An agent, which is usually chemical, that kills the growing organisms, it may not
affect bacterial spore.
Antiseptic: An agent that kills or inhibits the growth of microorganisms in contact with the body
without causing extensive damage to the body tissue and can be safely applied to living tissue.
Bacteriocidal agents: Agents which are able to kill bacteria.
Bacteriostatic agents: Agents which prevent multiplication of bacteria and they may remain alive.

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Factors influencing efficacy of a sterilant/ disinfectant
• Organism load
• Nature of organisms
• Concentration
• Nature of the Sterilant / disinfectant
• Duration of exposure
• Temperature
• Local environment

Classification of materials to be sterilized / disinfected

Earle H. Spaulding devised a rational approach to disinfection and sterilization of patient-care items
and equipment. This has three categories.

1. Critical Items
• Objects that enter sterile tissue or the vascular system.
• Confer a high risk of infection if they are contaminated with any microorganism.
• E.g. surgical instruments, cardiac and urinary catheters, implants, and ultrasound probes used in
sterile body cavities etc.

2. Semi-critical Items
• Objects that come in contact with mucous membranes or non-intact skin.
• E.g. respiratory therapy and anaesthesia equipment, some endoscopes, laryngoscope blades,
esophageal manometry probes, cystoscopes, anorectal manometry catheters, and diaphragm
fitting rings, etc.

3. Non-critical Items
• Objects that come in contact with intact skin but not mucous membranes.
• E.g. bedpans, blood pressure cuffs, crutches and computers, etc.

Methods of sterilization
The various methods of sterilization are:
1. Physical Method
- Thermal (Heat) methods

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 - Radiation method
- Filtration method
2. Chemical Method
3. Gaseous method

Physical methods
Heat sterilization
Heat sterilization is the most widely used and reliable method for materials, which are not damaged
by heat.
Two type of heat:
• Dry heat
• Moist heat

Dry Heat Sterilization:

It uses high temperatures to inactivate microorganisms. The benefit of dry heat includes good
penetrability and non-corrosive nature which makes it applicable for sterilizing glass-wares and
metal surgical instruments.

Examples of dry heat sterilization are:

1. Incineration
This is direct burning of materials at high temperature (800 – 1200 degree celcius). Burning to ashes.
Used for destroying materials such as:
- Soiled dressing
- Bedding of patient
- Animal carcasses
- Pathological materials

2. Red heat
It is a direct heating of an instrument or an object in a flame till it becomes red hot. Used for
sterilizing noninflammable materials such as:
- Tips of forceps
- Scissors

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3. Flaming
Direct exposure for a few seconds by passing a few times through the Bunsen flame without
allowing them to become red hot. May be used for:
- Scalpels
- Needles
- Cover slips
- Mouth of culture tubes
- Neck of flask

4. Hot air oven

Hot air oven is the most widely used method of sterilization by dry heat
Used to sterilize all glass syringes, Petri dishes, test tubes, flask, pipettes, cotton swabs, scalpel,
scissors, liquid paraffin, dusting powder, etc.

Moist Heat Sterilization:

Destroys microorganisms on an object by steam. It is more efficient than dry heat in penetrating the
material.
Moist heat may be used in three forms to achieve microbial inactivation
• Temperature below 100°C, e.g. pasteurization of milk, vaccine bath
• Temperature around 100°C, e.g. boiling
• Temperature above 100°C, e.g. autoclave

Autoclave
A machine that uses steam under pressure to kill harmful microbes on objects. In this apparatus,
material for sterilization is exposed to 121°C for 15 to 20 minutes at 15 lb pressure per square inch.

Uses
• All solids and liquid media
• Distilled water
• Saline solution
• Laboratory
• Swabs, syringes and needles
• Surgical instruments

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• Dressing material
• Pharmaceutical products

Chemical Methods
Chemical sterilization involves the use of certain chemicals to eliminate microbes. Those chemicals
that can be safely applied over skin and mucus membranes are called antiseptics.

An ideal antiseptic or disinfectant should have following properties:

• Should have wide spectrum of activity
• Should be able to destroy microbes within practical period of time
• Should be active in the presence of organic matter
• Should make effective contact and be wettable
• Should be active in any pH
• Should have long shelf life
• Should be speedy
• Should have high penetrating power
• Should be non-toxic, non-allergenic, non-irritative or non-corrosive

Classification of disinfectants:
1. Based on consistency
• Liquid (E.g. Alcohols, Phenols)
• Gaseous (Formaldehyde vapour)

2. Based on spectrum of activity

• High level
• Intermediate level
• Low level

3. Based on mechanism of action

• Action on membrane (E.g. Alcohol, detergent)
• Denaturation of cellular proteins (E.g. Alcohol, Phenol)
• Oxidation of essential sulphydryl groups of enzymes (E.g. H2O2, Halogens)
• Alkylation of amino-carboxyl- and hydroxyl group (E.g. Formaldehyde)

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 • Damage to nucleic acids (Formaldehyde)

Application of disinfectants
In Bacteriology
• For disposal of culture (3% Lysol)
• For preservation of sera, agar or phenol agar, vaccine, etc.

In Surgical Procedures
• Washing the hand
• To prepare and clean the area of operation
• To collect the blood under aseptic precautions
• For safe disposable of excreta and surgical dressing
• Cleaning of infected wounds
• For disinfection of used instrument.

In Hospitals
• To disinfect the operation theaters
• To disinfect costly equipment like endoscopes and cystoscopes etc.
• To control the spread of cross infection
• To disinfect linen and surgical dressing.

In Public Health Services

• For providing safe drinking water (e.g. chlorinated water)
• For disinfection of sewage before its disposal into the fields.

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 1.3. HOSPITAL WASTE MANAGEMENT

Objectives
At the end of this chapter, students should be able to:
• Define and classify hospital waste
• Describe the aim of hospital waste management
• Segregate and dispose waste materials appropriately
• Outline the universal precautions to follow when dealing with communicable diseases.

Introduction
Hospital waste management is a system that handles the segregation, containment, and disposal of
hazardous, hospital-generated, infectious waste. Efficient waste management is critical for healthcare
institutions because hospital waste can be pathogenic and environmentally hazardous.

Hospital waste refer to all waste, biological or non-biological that is discarded and is not intended
for further use in the hospital.

Mainly, hospital waste is of the following types:

Infectious waste: This type of waste of the hospital is harmful and may cause infectious diseases.

Non-infectious waste: It is the waste of the hospital that is non-infectious. This category of hospital
waste does not cause any harm.

Infectious waste of hospital and laboratory

• Microbiology waste
• Blood and body fluids
• Used sharps
• Pathological waste, i.e. samples and tissues
• Bandages and cotton swabs
• Animal carcasses
• Beddings.

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Common infectious microorganisms associated with hospital or Laboratory
• HIV
• Hepatitis B
• Mycobacterium tuberculosis
• Pseudomonas Aeruginosa

Chief objectives of hospital waste management:

• To prevent injury
• To prevent accidental transmission of microbial infection to hospital staffs, patient, attendants of
patients, visitors and general public

Segregation of hospital waste in Namibian hospitals

Hospital waste is segregated and disposed of as under:

1. Yellow plastic bags and containers: left over food

2. Red plastic bags and containers: infectious waste material, sent for sterilization. Thereafter they
are disposed of by land filling. E.g. infected dressings
3. Green plastic bags and containers: soiled linen
4. Black plastic bags and containers: general waste
5. Safety boxes: for sharps
6. Transparent puncture proof container: empty vials and ampoules

Disposal of hospital and laboratory waste

1. Land filling
2. Burial
3. Sewage draining
NB: Waste in fluid form can be discarded in sewage drains. Apart from this treatment, incineration is
also a vital method of disposal.

Universal precautions to follow in order to prevent transmission of nosocomial infections.

1. Consider all patients and clinical specimens potentially infectious especially for AIDS, Hepatitis
B, etc.

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2. All specimens especially blood must be dispensed in leak proof impervious bags for
transportation.
3. Use of gloves, face mask with glasses while handling blood or fluid specimens.
4. Wear proper laboratory coats while working in the laboratory.
5. Pipetting by mouth must not be done.
6. Decontaminate the laboratory working surface with decontaminant after completion of laboratory
procedures.
7. In case of spillage of blood or other specimen treat the surface with appropriate disinfectant.
8. Biological safety hood must be used for laboratory procedures.
9. All potentially contaminated material should be decontaminated before disposal or reuse.
10. Remove all protective wearing/clothing before leaving the laboratory or attending the patients in
operation theater

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 1.4. INFECTIONS

Objectives
At the end of this chapter, students should be able to:
• Define Infection and Disease
• Identify various types of infections
• Discuss the epidemiological pattern of infections
• Mention the various sources of human infections
• Describe the various routes by which transmission of infection occurs

Introduction
Infection is the biological process, which takes place in the body of organisms following the
penetration of pathogenic microorganism, resulting in obvious or latent disease or in a carrier state.

Definitions
Infection: The invasion and multiplication of microorganism in the tissue of host.
Disease: Damage or injury produced by microorganism that impairs host function.
Pathogenicity: The ability of microbial species to produce disease.
Virulence: The ability of microbial strains to produce disease, e.g. polio virus contains strain of
varying degree of virulence.

Various types of Infections

1. Primary infection: Initial infection caused by microorganism.
2. Reinfection: Subsequent infection by same pathogen in a host.
3. Secondary infection: Infection by a new organism, in a host whose resistance is lowered by pre-
existing infectious disease.
4. Mixed infection: When more than one microorganism causes infection simultaneously.
5. Focal infection: It is a condition where due to infection at localized sites like appendix and
tonsils, general effects are produced.
6. Cross infection: When a patient is already suffering from a disease and new infection is set up
from another host or external source.
7. Nosocomial infection/ hospital acquired infection: Cross infection occurring in hospital.
8. Iatrogenic infection: Infections acquired during diagnostic or therapeutic procedures.

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Classification of infections based on clinical effects they produce:
• Symptomatic or apparent infections: Infection that produces noticeable symptoms. It may be
classified into:
- Acute infection: The symptoms last for a short term period.
- Chronic infection: The symptoms persist for a long period.
• Asymptomatic or in-apparent or subclinical infection: It is an infection that is active but does
not produce noticeable symptoms.
• Atypical infection: Infections in which typical or characteristic manifestations of a particular
disease are not present.
• Latent infection: It refers to an infection that is inactive or dormant or in hidden form; but
capable of reactivating later.

Classification of infection based on source:

• Endogenous infection: The source of infections is within the body.
• Exogenous infections: The source is outside the host’s own body.

Epidemiological pattern of infection

Four epidemiological terms are often used to describe infection:
• Endemic: The infections that occur at a persistent, usually low level in a certain geographical
area. E.g., Malaria is endemic to the tropical regions of Africa.
• Epidemic: The infections that occur at a much higher rate than usual in a particular geographic
area. E.g., Hep E in Windhoek 2017/2018
• Pandemic: Infection that spread rapidly over large areas of the world. E.g., Global Covid-19
pandemic.
• Sporadic: Infections occur at irregular intervals or only in a few places; scattered or isolated.

Sources of human infections

• Humans: commonest source.
• Animals: Infectious diseases transmitted from animals to man are called zoonosis.
• Insects: The disease caused by insects are called arthropod borne disease. Insects like
mosquitoes, fleas, lice that transmit infection are called vector. Some vectors may act as reservoir
host (e.g. ticks in relapsing fever and spotted fever).
• Soil: Soil may serve as source of parasite infection like roundworm and hookworm.

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• Water: Vibrio cholerae, infective hepatitis virus (Hepatitis-A)
• Food: Contaminated food may be source of infection e.g Salmonella Typhi.

Various routes by which transmission of infection occurs

1. Transmission through air (inhalation)
Infection is transmitted through inhaling infectious droplets or particles.
Examples: tuberculosis, influenza, measles, mumps, smallpox, etc.

2. Contact
Direct contact: sexual intercourse, kissing, close body contact, e.g., syphilis, gonorrhoea, etc.
Indirect contact through the agency of fomites.
-Transmission of diphtheria in school children by sharing of pencils.

3. Ingestion
Gastro – intestinal tract infections are generally transmitted by ingestion of contaminated food or
water.
Infections transmitted by ingestion may be:
- Water borne, e.g. Cholera
- Food borne, e.g. food poisoning
- Hand borne, e.g. dysentery

4. Insects
They act as vectors and transmit infections from one person to another.

5. Inoculation
Transmission of pathogenic may occur by direct deposition of causative agent in tissue:
- Transmission of rabies virus by dog
- Transmission of arboviruses by insect vectors

6. Iatrogenic transfer
During diagnostic or therapeutic procedures such as: catheterization, injection, lumbar puncture,
dialysis, etc.

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7. Congenital
Transmission of infections from mother to fetus in utero by crossing the placental barrier. E.g.,
Treponema pallidum, HIV, Rubella virus, Plasmodium spp

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 1.5. NORMAL MICROBIAL FLORA

Objectives
At the end of this chapter, students should be able to:
• Describe normal flora
• Enlist the Advantages and Disadvantages of flora
• Describe the normal flora of various parts of the body

Introduction
Internal tissues including blood, brain, muscle, etc. in a healthy person are often clear of germs.
Skin and mucous membranes, which are surface tissues, are continuously in contact with
environmental organisms and are therefore easily colonised by different microbial species.

Normal Microbial Flora

The term normal microbial flora refers to the population of microorganisms that inhabit the
skin and mucous membranes of healthy normal persons.
• The resident flora consists of relatively fixed types of microorganisms regularly found in a
given area at a given age; if disturbed, it promptly re-establishes itself.
• The transient flora consists of non-pathogenic or potentially pathogenic microorganisms
that inhabit the skin or mucous membranes for hours, days, or weeks; it is derived from the
environment, does not produce disease, and does not establish itself permanently on the
surface.

Resident flora
Advantages
• They prevent the entry of pathogens.
• These synthesize vitamins especially Vitamin K and several B Group vitamins.
• Stimulates the production of antibodies.
• Play a role in the defense mechanism of the body.

Disadvantages
• They become pathogenic when the immunity is lowered.
• They may act as pathogens in different tissue (other than their normal habitat) e.g. normal
flora of intestine may cause urinary tract infection (UTI).
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• May cause confusion in laboratory diagnosis.

Examples of normal microbial flora

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 UNIT 2: IMMUNOLOGY

The human body is constantly exposed to a wide variety of pathogens. In this unit, we are
going to learn some of the ways in which the body defends itself.

Definitions
Immunology - The study of the physiological mechanisms that humans use to defend their
bodies from invading organisms, e.g. bacteria, Viruses, Fungi, Parasites and Toxins.
Immune system - all the body organs and processes of the body that fights against diseases.
Immunity
It is the ability of the body to resist and fight against diseases and infections.

2.1. IMMUNITY, ANTIGEN (AG), IMMUNOGLOBULIN’S(IGS) – ANTIBODIES

(ABS)

Objectives
At the end of this chapter, students should be able to:
• Explain different types of immunity

Types of immunity
1. Innate immunity
2. Acquired (adaptive) immunity

Innate immunity / Natural immunity

The inborn capacity of the body to resist pathogens.
- Resistance possessed by an individual at birth.
- Provide first line of defense against infections. This means it prevents the microbes from
entering the body, e.g. skin and mucous membrane.
- Whenever the microbes happen to enter the body, innate immunity provides second line of
immunity which involves different blood cells and proteins that fights against these
microbes.

Adaptive immunity (Acquired immunity)

The immunity which develops throughout our lives.

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• Adaptive immunity is divided into: adaptive active immunity and adaptive passive
immunity.

Adaptive active immunity

The production of antibodies against a specific disease by the immune system.
• Naturally acquired through disease
• Artificially acquired through vaccination
• Vaccines include inactivated toxins, killed microbes, parts of microbes, and viable but
weakened microbes.
• Produces memory cells that protect the body from future infection by the same microbe
• Protection for active immunity is permanent.
• Active immunity takes several weeks to become active but passive is immediate

Adaptive passive Immunity

Protection against disease through antibodies produced by another human being or animal.
• Ex. Maternal antibodies from mother to child
• Passive immunity doesn’t last as long as active immunity (only weeks or months):
• No lymphocytes are stimulated to clone themselves
• No memory cells have been made
• Effective, but temporary as this type of immunity can only last as long as the
antibodies/toxins last in the blood
• Passive immunity can be transferred artificially by injecting antibodies from an animal that
is already immune to a disease into another animal

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Antigen(Ag)
An antigen is any foreign substance that causes the immune system to produce antibodies
against it.
Examples of antigens include toxins, chemicals, drugs and other products produced by viruses,
bacteria, protozoa

Antibody
A disease fighting protein developed in response to the presence of an antigen.
Function:
• To bind its antigen in order to kill or neutralize in collaboration with others components of
the immune system.

The antibody-antigen reaction/bonding

The antigens and the antibodies combine specifically with each other. This interaction is called
antigen-antibody reaction

Immunoglobulin (Ig)
- Immunoglobulins are antibodies/ glycoprotein molecules produced by plasma cells (white
blood cells), e.g. Ig A (alpha), Ig G (gamma), Ig M (mu).

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 2.2. IMMUNE SYSTEM

Objectives
At the end of this chapter, students should be able to:
• Identify subdivisions of immune system
• Explain the structure of immune system
• Identify the organs of the immune system

Functions of a healthy immune system:

1. Constant surveillance of the body
2. Recognition of foreign material
3. Destruction of entities deemed to be foreign

Four major subdivisions of immune system are:

1. Reticuloendothelial system (RES)
2. Extracellular fluid (ECF)
3. Bloodstream
4. Lymphatic system

Reticuloendothelial system (RES)

• Network of connective tissue fibers that interconnects other cells and meshes with the
connective tissue network surrounding organs.
• Inhabited by phagocytic cells that attack and ingest microbes.

Extracellular fluid(ECF)
• Provides a route for return of extracellular fluid to the circulatory system
• Acts as a drain-off system for the inflammatory response
• Renders surveillance, recognition, and protection against foreign material

Blood stream
• Whole blood consisting of plasma and blood cells (red blood cells and white blood cells.
• White blood cell consists of: neutrophils, eosinophils, basophils, lymphocytes,
macrophages.

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Lymphatic system
• Transports white blood cells, fats, cellular debris and infectious agents

Structure of the immune system

Parts of the immune system

Primary (central): Provide appropriate environment for development and maturation of
lymphocytes
Secondary (peripheral): site where mature lymphocytes can interact effectively with those
antigens.

Primary organs (thymus and bone marrow)

Thymus
• A bilobed organ located above the heart near the throat
• Produces thymic lymphocytes
Bone marrow
• Located in the middle of the bones, specifically the vertebrae, pelvic, leg bones
• It generates T-cells, B-cells, and macrophages

Secondary (peripheral)
1. Lymph nodes
• Located along the course of the immune system

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• Act as filter for foreign particles including cancer cells
• Become inflamed or enlarged in various diseases.
2. Spleen
• Found in the upper left part of the abdomen
• It removes old blood cells and store the white blood cells
3. Mucosa associated lymphoid tissue
• A diffuse system of small concentrations of lymphatic tissue.

Cells of the immune system

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 2.3. IMMUNE RESPONSE

Objectives
At the end of this chapter, students should be able to:
• Understand the nature of immune responses
• Define immune responses
• Understand and describe different types of immune responses

Immune response

• The specific reactivity induced in a host by an antigenic stimulus is known as immune

response
• The immune response can be of two types:
- Humoral mediated immunity (HMI)
- Cell mediated immunity (CMI)

Humoral immune response

• Antibodies are produced in response to antigens

Cell mediated immune response

• Does not involve antibodies

• Involve many types of immune cells and cytokines,
• Protect against fungi and viruses
• Provide immunity against cancer

First line of immune defense (Physical and chemical barriers)

• The skin prevents pathogens from entering the body

• Skin gland (oil and sweat) secret chemicals that produce a pH of 3-5 causing delay in the
growth of bacteria
• Mucous in body organs (e.g., lungs, digestive system) traps microorganisms
• Cilia in the respiratory tract sweep away the microorganisms
• Tears and saliva secrete an enzyme called lysosomes that breakdown bacterial cell walls
• Stomach acid kills microorganisms in wallowed with food and drinks

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Second line of defense

• Inflammatory response
• When microorganisms penetrate the skin, digestive or urinary tract it results in
inflammation
• Damaged cells release chemical signals such as histamine that increases capillaries blood
flow into affected area.
• The increases heat and raises the mobility of white blood cells
• Pathogens are attacked and destroyed by pathogens
• Natural killer cells
• Kills virus infected cells

Complement system

• Proteins that work with antibodies

• They cause bursting of cells and send signals to phagocytes that a cell need to be removed

30
 2.4. HYPERSENSITIVITY

Objectives
At the end of this chapter, students should be able to:
• Define hypersensitivity
• Mention the types of hypersensitivity

Hypersensitivity
Refers to undesirable reactions produced by normal immune system e.g allergies and
autoimmunity.

Classification of hypersensitivity
Type I (Immediate hypersensitivity)
Type II (cytotoxic hypersensitivity)
Type III (immune complex hypersensitivity)
Type IV (delayed hypersensitivity)

31
 2.5. IMMUNIZATION AND IMMUNIZATION SCHEDULE

Objectives
At the end of this chapter, students should be able to:
• Differentiate between immunization and vaccination
• State the different types of immunizing agents
• Know the national immunization schedule

Immunization
The process of stimulating the body to produce antibody and other immune responses through
administration of vaccine or toxoid.
Vaccination- the process of inoculating the antigen(vaccine) into the body.

Immunizing agents
• Vaccines
• Immunoglobulin
• Antitoxins /antisera

National Immunization Schedule

The schedule should be planned according to the need of the community
It must be effective, feasible and acceptable by the community.

IMMUNIZATION SCHEDULE FOR CHILDREN UNDER FIVE YEARS

AGE VACCINE AGAINST DOSA MODE SITE

GE

At birth ½ up to 11 BCG ½ Tuberculosis ½ 0.05ml Intra-dermal (L) upper

months ½ ½ ½ arm ½ at the
b-OPV 0 ½ Poliomyelitis½ insertion ½
At birth ½ up to14 days 2 drops Orally ½ of the deltoid
½ Hep B 0 ½ Hepatitis B ½ ½ muscle ½
-------

32
Within 24 hours½ of 0.5 ml Intramuscular
birth½ ½ ½ Lateral
middle third
½ of (L)
thigh½

On 6 weeks ½ or first b-OPV 1 ½ Poliomyelitis ½ 2 drops Orally ------

contact after 6 weeks ½
DPT1+ Diphtheria ½ 0,5ml Intramuscular Lateral
Hep B1 + Pertussis ½ ½ ½ middle third
Hib1 ½ Tetanus½ ½ of (L)
(Pentavalent) Hepatitis B ½ thigh ½
Haem.influ. type
b½
Rotavirus 1½
Rotavirus ½ 2 doses Orally ½ --------
PCV 1½ ½
Pneumococcal ½ Intramuscular Lateral
0,5ml ½ middle third
½ ½ of (R)
thigh ½

On 10 weeks ½ or 4 b-OPV 2 ½ 2 drops Orally -----------

weeks after b-OPV1, Lateral
Pentavalent1 Pentavalent 2 0,5ml Intramuscular middle third
Rotavirus 1 and PCV 1 ½ Orally of (L) thigh
½ Rotavirus 2 2 doses Intramuscular -----------
½ PCV 2 ½ Lateral
0,5ml middle third
of (R) thigh

33
On 14 weeks ½, or 4 b-OPV 3 ½ 2 drops Orally ------------
weeks after b-OPV2,
Pentavalent 2 IPV ½ Poliomyelitis ½ 0,5ml Intramuscular Lateral
Rotavirus 2 and PCV 2 ½ ½ middle third
½ Pentavalent 3 of (R) thigh
½ 0,5ml Intramuscular ½
Lateral
PCV 3 ½ 0,5ml Intramuscular middle third
of (L) thigh;
Lateral
middle third
of (R) thigh

On 9 months ½ or first Measles ½

contact after 9 months Rubella Measles ½ 0,5ml Subcutaneous (R) upper
of age ½ or at 6 months ½(MR) Rubella½ ½ ½ arm ½
½ during measles deltoid
epidemics ½ muscle ½
Measles½ 0,5ml Subcutaneous (R) upper
On 15 months ½ Rubella½(M arm,
R) deltoid
muscle

On 5-year ½ or first b-OPV ½ Poliomyelitis ½ 2 drops Orally ½ --------------

contact before 10 years DT ½ Diphtheria ½, 0,5ml Intramuscularl Lateral
½ Tetanus ½ ½ y½ middle third
½ of (L)
thigh ½

On ten-year ½ or first b-OPV ½ 2 drops Orally ----------------

contact before 15 years DT ½ 0,5ml Intramuscularl ---
½ y

34
 Lateral
middle third
of (L) thigh

%
Note: Hep B 0 (Hepatitis B) dose should be given within 24 hours of birth
OPV 0 (Oral Polio Vaccine 0) dose should be given within 14 days of birth
BCG (Bacillus Calmette Guérin) dose should not be given after 12 months of age
RV1 (Rotavirus 1) dose should not be given after 24 weeks of birth
IPV (Inactivated Polio Vaccine) dose is only given once at 14 weeks

35
 UNIT 3: BACTERIOLOGY

Objectives
At the end of this unit, students should be able to:
• Define bacteriology
• Identify different bacterial infections
• Describe different preventative measures of different bacterial infections

Bacteriology is the study of bacteria and their characteristics.

Staphylococcus
Clinical findings(symptoms)
• Localized Staph infection which appears as a pimple,
• Hair follicle infection, or abscess
• Impetigo
• Deep lesions, e.g. bones, joints, deep organs, and soft tissues
• Scalded skin syndrome: due to exfoliation.

Treatment
• Most boils resolve without antimicrobial therapy
• Deeper ones require both surgical drainage antimicrobial treatment
• Penicillins and cephalosporins
• Vancomycin, clindamycin or erythromycin

Streptococcus
Infections
• Streptococcal pharyngitis
• Scarlet fever
• Impetigo

Treatment:
• Penicillin, Erythromycin, Azithromycin

36
 Pneumococcus

Infections
• Meningitis
• Pneumonia

Treatment
• Sulfonamides, Penicillin

Clostridium

Four major clostridial species

1. Clostridium perfringens: gas gangrene, food poisoning
2. C. tetani: tetanus
3. C. botulinum: botulism
4. C. difficile: pseudomembranous colitis

Treatment:
• Administration of massive doses of penicillin

Prevention:
• Proper food preparation
• Boiling contaminated water
• Immediate cleansing of wounds
• Debridement of disease tissue

Neisseria
Neisseria meningitis
• Causes meningococcal infection

Signs and symptoms

• Fever
• Headache
37
• Stiff neck
• Nausea
• Vomiting
• Photophobia (eyes being more sensitive to light)
• Altered mental status (confusion)

Treatment
• Administration of penicillin
• Meningococcal vaccine

Neisseria Gonorrhea
• Causes Gonorrhea

Infections
• Gonorrhea- purulent discharge for involved site (e,g urethra, cervix, anus)
• Neonatal conjunctivitis (purulent discharge/ocular infection by neonate at birth
• Pelvic inflammatory Disease (PID)

Signs and symptoms

Gonorrhea often has no symptoms, but it can cause serious health problems, even without
symptoms.

Women who do have symptoms may have:

• Painful or burning sensation when peeing;
• Increased vaginal discharge; and
• Vaginal bleeding between periods.

Men who do have symptoms may have:

• A burning sensation when peeing;
• A white, yellow, or green discharge from the penis; and
• Painful or swollen testicles (although this is less common).

Treatment
• Penicillin, tetracycline
38
• In neonates, prophylaxis with 1%silver nitrate

Vibrio Cholerae
Infections
• Cholera - an acute diarrheal illness caused by infection of the intestine with bacteria Vibrio
Cholerae
• People can get sick when they swallow food or water contaminated with cholera bacteria.

Treatment
• Antibiotics, zinc supplements

Signs and symptoms

• Profuse watery diarrhea, sometimes described as “rice-water stools”
• Vomiting
• Thirst
• Leg cramps
• Restlessness or irritability

Spirochetes

Treponema pallidum
• A spirochete that causes Syphilis.

Syphilis is a systematic, sexually transmitted disease.

Transmission
1.Acquired syphilis:
This is when T. palladium enters the body via body fluids.
• This can be through a cut or break in the skin or mucous membranes (external genitalia or
mouth)
• It can be through sexual contact (oral, anal or vaginal)
• Through contaminated needles
• Direct contact with a skin lesion

39
2.Congenital syphilis
Wwen a mother has syphilis and the spirochetes infects the baby in the uterus or when exiting
through the vagina.

Stages of acquired syphilis

1. Primary (early localized)
• Acquired syphilis stages starts from 1-3 weeks after the spirochete’s lands on skin or
mucous membrane
• The spirochete destroys the tissue and this result into a painfulness chancre
• These chancres heal on their own in few months
• Some spirochetes travel to lymph node causing inflammation(lymphadenopathy) and enters
the blood

2. Secondary (disseminated stage)

• Occurs 6-1 weeks after infection
• The spirochetes enter the body causing spirochete-emia
• Causing non-itchy rash throughout the body
• Symptoms includes, headache, fever, pustules, anorexia, malaise, temporary alopecia

3. Latent (asymptomatic)
• The spirochetes enter the organ capillaries
• This stage is divided into early phase and late phase

Early stage:
• Occurs within a year of infection
• Spirochetes circulate in blood causing symptoms of the secondary stage

Late phase:
• Occur after a year of infection
• Spirochetes stay in the capillaries of organs and tissues
• Few spirochetes circulate in blood but cause severe immune response
• This leads to the tertiary stage

40
4. Tertiary stage
• Characterized by type IV hypersensitivity reaction
• This leads to swelling, edema, fever and redness
• Development of gumma
• Tertiary syphilis causes organ damage such as the heart, joints, brain etc

Congenital syphilis
• The spirochetes are transmitted from a mother to a fetus/baby through the placenta or
during childbirth
• The child might die in the womb
• Or the baby will be born with maculopapular rash in palms and feet sore
• It is also characterized by snuffles (increase in mucous secretion), damage to liver, spleen
and eyes.

Late disease
After 2 years the child might develop the following features:
• Saddle nose
• Saber shins
• Hutchinson teeth
• Hearing loss

Treatment
• Administration of penicillin and doxycycline

41
 UNIT 4: MYCOBACTERIA

Objectives
At the end of this unit, students should be able to:
• Define Mycobacteria
• Understand Mycobacterial infections common in humans (M. Tuberculosis, M. Leprae)

Mycobacteria are a type of bacteria with thick cell walls. They are known to stay dormant for
decades, surviving harsh conditions and treatment with antibiotics.

Mycobacteria Tuberculosis
• Causes tuberculosis (TB).
• Usually attacks the lungs, but can attack any part of the body such as the kidney, spine, and
brain.
• Two TB-related conditions exist: latent TB infection (LTBI) and TB disease.

The Difference between Latent TB Infection (LTBI) and TB Disease

A Person with Latent TB Infection A Person with TB Disease

• Has no symptoms • Has symptoms that may include:
- a bad cough that lasts 3 weeks or
longer
- pain in the chest
- coughing up blood or sputum
- weakness or fatigue
- weight loss
- no appetite
- chills
- fever
- sweating at night
• Does not feel sick • Usually feels sick
• Cannot spread TB bacteria to others • May spread TB bacteria to others

42
 • Usually has a skin test or blood test
result indicating TB infection
• Has a normal chest x-ray and a
negative sputum smear
• Needs treatment for latent TB
infection to prevent TB disease
• Usually has a skin test or blood test
result indicating TB infection
• May have an abnormal chest x-ray, or
positive sputum smear or culture
• Needs treatment to treat TB disease

Transmission
• Through the air from person to person

Diagnosis
• Bacteriological test
• Culture test
• Radiography
• Tuberculin skin test

Prevention
• Using mask
• Regular medical follow up
• Isolation of patient
• Natural sunlight
• Ventilation

Mycobacterium Leprae
• Causes Leprosy (Hansen’s disease).
• M. leprae multiplies slowly and the incubation period of the disease, on average, is 5 years.
• Symptoms may occur within 1 year but can also take as long as 20 years or even more.
• Mainly affects the skin, the peripheral nerves, mucosa of the upper respiratory tract, and the
eyes.
• The disease is curable with multidrug therapy
• Untreated, leprosy can cause progressive and permanent damage to the skin, nerves, limbs,
and eyes.

43
Transmission
• Spreads through infected respiratory droplets
• Can infect others by entering breaks in the skin

44
 UNIT 5: VIROLOGY

Objectives
At the end of this unit, students should be able to:
• Define Virology
• Identify viral infections
• Explain the transmission and prevention of different types of viral infections

Introduction
The importance of virology has been observed throughout time in the form of viral outbreaks,
epidemics, and pandemics.

Virology is the branch of microbiology which mainly deals with the study of various types of
viruses, including their characteristics, agents, viral diseases, etc.

Herpes Viruses
• Herpes is a common viral infection that is spread through skin-to-skin contact.
• Herpes outbreaks usually show up as one or more little sores on the mouth, genitals or
anus.

Types
• herpes simplex type 1 (HSV-1)/ oral herpes
• herpes simplex type 2 (HSV-2)/ genital herpes

Transmission
• HSV type 1 (HSV-1) is typically transmitted by oral-to-oral contact with the virus in sores,
saliva or surfaces in or around the mouth and causes infection in or around the mouth (oral
herpes), but it can also cause genital herpes.
• HSV-2 is mainly sexually transmitted and causes genital herpes.

Signs and symptoms

Oral herpes:
• Infection is mostly asymptomatic, but symptoms can include painful blisters or open sores
(ulcers) in or around the mouth (cold sores).

45
• Tingling, itching or burning sensation around their mouth before the appearance of sores.
Genital herpes:
• Can be asymptomatic or have mild symptoms that go unrecognized.
• When symptoms occur, genital herpes is characterized by one or more genital or anal
blisters or ulcers.
• Additionally, symptoms of a new infection often include fever, body aches and swollen
lymph nodes.

Treatment
• Antiviral medications – such as acyclovir, famciclovir and valacyclovir – are the most
effective medications for people infected with HSV.
• These can help to reduce the severity and frequency of symptoms but cannot cure the
infection.

Prevention
• Avoid oral contact with others (including oral sex) and sharing objects that touched saliva.
• Abstain from sexual activity
• Consistent and correct use of condoms
• Medical male circumcision

Hepatitis viruses
Hepatitis is a medical condition defined by the inflammation of the liver caused by hepatitis
viruses.
Classification of hepatitis

46
 Influenza Virus
Influenza is commonly called “the flu’ caused by the influenza virus that infect the respiratory
tract.

Types
• Influenza A (causes swine influenza and avian influenza)
• Influenza B
• Influenza C (causes a very mild respiratory illness or no symptoms at all)
Symptoms
• Fever, cough, sore throat, runny nose, extreme fatigue
Transmission
• Person to person through sneezing coughing or talking
Prevention
• Flu shots
• Nasal-spray flu vaccine

Rabies Virus
• Rabies is disease caused by rabies virus that causes acute or severe encephalitis.
• Also called “hydrophobia”
Transmission
• When bitten by rabid animal
• Handling infected animals
Symptoms
• Sore throat
• Headache, fever, hallucination, inability to swallow water

Measles Virus
• Measles is highly infectious illness caused by a measles virus
• The virus lives in the mucus of the nose and throat of people

Symptoms
• Fever, sore eyes, runny nose. White spots in the mouth, harsh dry cough, red rash

47
Prevention
• Vaccination
• Keep affected children out of school for 7days strict isolation with concurrent disinfection.
• Well ventilated room

Poliomyelitis Virus
• Poliomyelitis often called polio or infantile paralysis is an infection that causes nerve injury
which leads to partial or full paralysis.
• This infection is caused by poliomyelitis virus

Transmission
• Person to person via fecal -oral route
• Through oral-oral route
Prevention
• Practicing hygiene
• Encouraging good sanitation practices
• Polio vaccine

HIV (human immune-deficiency Virus)

• A virus that causes AIDS
• HIV cause damage to your immune system, and interferes with your body's ability to fight
infection and disease.

Transmission
• Through unprotected sex (anal or vaginal sex without a condom).
• By sharing needles or other equipment to inject drugs (including steroids).
• To a fetus or baby during birth, or breastfeeding.

Prevention
• Practice safe sex
• Limit your number of sexual partners.
• Talk to your health care provider about pre-exposure prophylaxis (PrEP)
• Pregnant women with HIV should take medication to protect their babies

48
 UNIT 6: MYCOLOGY

Objectives
At the end of this unit, students should be able to:
• Define mycology as the study of fungus
• Identify fungal infections
• Explain the transmission and prevention of different types of fungal infections

Introduction
Mycology has become an important area of research in clinical microbiology as of the
approximately 70,000 recognized species of fungi, about 300 are known to cause human
infections.

Mycology studies fungi: their structure, genetic composition, biochemical properties,

taxonomy, and their applications.
Fungi- are eukaryotic organisms that exist as saprophytes.

Types of fungi

Candida
Diseases caused:
• Urinary tract candidiasis
• Pulmonary candidiasis
• Meningitis

Habitant: mostly part of the normal flora of humans (GIT, vagina mucosa, skin nails)

Transmission
• Mostly endogenous infection
• Less common exogenous infection (contaminated hospital equipment)

Cryptococcus
Habitant: occur worldwide, ubiquitous soil saprophyte
Transmission: inhalation

49
Diseases caused:
• Genital cryptococcosis
• Primary cryptococcal pneumonia
• Cutaneous cryptococcosis
• Pulmonary cryptococcosis

Dermatophytes
Habitant: soil
Transmission: direct contact or indirect contact through formites
Diseases:
• Tinea corporis (body)
• Tinea cruris (groins)
• Tinea pedis (feet)
• Tinea magnum (hands)
• Tinea capitis (scalp)
• Tinea unguium (nails)
• Tinea barbae (bears)

Aspergillus
Habitant: air, soil and decaying matter
Transmission: inhalation

Diseases caused:
• Allergic reaction
• Allergic sinusitis: nasal obstruction and discharge, facial pain
• Bronchial pulmonary form: asthma

50
 UNIT 7: PARASITOLOGY

Objectives
At the end of this unit, students should be able to:
• Define Parasitology
• Discuss the classification of parasites
• Identify parasitic infections
• Explain the transmission and prevention of different types of parasitic infections

Introduction
A large number of infections of humans are caused by parasites which range from relatively
benign to fatal with some parasitic diseases being the cause for major human health problems
throughout the world.

Parasitology is the study of parasites and their relationship to their Host

Parasite/Parasitism – One partner/a living organism takes benefit/nourishment
and other needs from a Host, thereby causing harm.

Classification of parasites
A. According to their habitat:
1. Ectoparasites: parasites living on or affecting the skin surface of the host. E.g. lice, tick, etc.
2. Endoparasites: Parasites living within the body of the host, e.g. Leishmania species,
Ascaris lumbricoides, etc.

B. According to their dependence on the host:

1. Permanent (obligate) parasites: The parasite depends completely upon its host for
metabolites, shelter, and transportation. This parasite cannot live outside its host. E.g.,
Plasmodium species, Trichomonas vaginalis, etc.
2. Temporary (facultative) parasite: The parasite is capable of independent existence in
addition to parasitic life, e.g. Strongyloids stercolaris, Naegleria fowleri, etc.

C. According to their Pathogenicity:

1. Pathogenic parasites: It causes disease in the host, e.g., E. histolytica
2. Non-Pathogenic (commensal) parasite: The parasite derives food

51
and protection from the host without causing harm to the host, e.g. Entamoeba coli
3. Opportunistic parasites: Parasites which cause mild disease in immunologically healthy
individuals, but they cause severe disease in immuno-deficient hosts e.g. Pneumocystis carnii,
etc.

Modes of transmission
- Direct contact - Saliva, Blood, Urine, Mucous
- Indirect contact – Animal houses
- Vector-borne - Ticks, Mosquitoes; Tsetse flies
- Foodborne

Entamoeba histolytica
Geographical distribution: Cosmopolitan distribution, mainly in the tropics and subtropics.
Habitat: Trophozoite: - Large intestine, liver abscesses and other extraintestinal
organs
Cyst: Found in the stools of chronic dysenteric patients and carriers.

Mode of Transmission
Infective stage: Tetra-nucleated mature cyst.
Man acquires infection of E. histolytica from:
- Ingestion of food or drink contaminated by infective cyst.

Clinical Features and Pathology

• May be asymptomatic or exhibit amoebic dysentery or extra-intestinal amoebiasis in the
liver, brain, spleen, lung, etc.
• Amoebic dysentery occurs when E histolytica trophozoites invade the wall of the large
intestine and multiply in the submucosa, forming large flask shaped ulcers.
• The amoeaba ingest red cells from, damaged capillaries.

Prevention and Control

• Cooking of food and vegetables
• Hand washing after defecation and before eating
• Safe water supply (treatment, boiling, filtration, etc.)
• Proper sanitary disposal of faeces.
52
• Treatment of infected individuals and health education.

Necator americanus (Hookworm)

Geographical Distribution: Wide spread in the western hemisphere. It is the predominant
species in all parts of the tropics. For East, South Asia, pacific Islands, Tropical Africa, Central
and South America.

Habitat:
Adult: Jejunum and less often in the duodenum of man
Eggs: In the faeces; not infective to man
Infective larvae: Free in soil and water

Pathology: causes hookworm infection.

Major symptoms are:

• Severe itching at the site of skin penetration known as "ground itch",
• Mild pneumonia with cough, sore throat, bloody sputum, headache, weakness, bloody
diarrhea and anemia.
• Adult hookworm causes chronic blood loss. It has been estimated that a
• single N. americanus ingests about 0.03ml.

Prevention and control

• Sanitary disposal of faeces
• Wearing adequate protective foot ware
• Treatment and health education.

Ascaris Lumbricoides (Roundworm)

Geographical Distribution: Cosmopolitans. A. lumbricoides is one of the commonest and
most widespread of all human parasites.
Habitat:
Adult: In the small intestine
Egg: In the faeces

53
Pathology:
• During their migration, Ascaris larva can cause inflammatory and hypersensitive reactions
including pneumonia like symptoms, attacks of coughing, and bronchial asthma.
• Developing and mature worms in the intestine frequently cause pain, nausea, diarrhea and
vomiting.
• Its infection in children is known to affect gastrointestinal function. Infected children are
often Vitamin A deficient and have low serum albumin levels.
• Frequent exposure to infection may result in impairment of physical and intellectual
development.

Prevention and Control

• Prevent soil contamination by sanitary disposal of faeces in latrines
• Washing hands before eating
• Avoid eating uncooked foods such as vegetables, green salads
• and fruits
• Treatment and health education.

Malaria
• Malaria is an acute febrile illness caused by Plasmodium parasites, which are spread to
people through the bites of infected female Anopheles mosquitoes.
• There are 5 parasite species that cause malaria in humans, and 2 of these species – P.
falciparum and P. vivax – pose the greatest threat. P. falciparum is the deadliest malaria
parasite and the most prevalent on the African continent. P. vivax is the dominant malaria
parasite in most countries outside of sub-Saharan Africa.

Transmission of Malaria:
• Bite by infected female Anopheles mosquitoes.
• Congenital/Transplacental
• Contaminated syringes and needles
• Blood transfusion/organ transplant

Malaria can either be:

1. Asymptomatic – no symptoms (due to acquired immunity)

54
2. Simple Malaria/Uncomplicated Malaria
- Fever is the most common symptom.
- Headache, aching joints, back pain, nausea, vomiting, and general
discomfort

3. Severe Malaria/ Complicated Malaria

- Severe anaemia
- Cerebral malaria,
- Coma or altered level of consciousness
- Drowsiness or lethargy
- Prostration
- Acute pulmonary oedema (adult respiratory distress
- syndrome)
- Hypotension and shock
- Persistent/excessive vomiting

Prevention and Control

1) Avoid mosquito bites by:
- Selecting healthy sites for houses and screening windows and doors with mosquito net.
- Using mosquito bed nets and mosquito repellents
- Wearing protective clothes such as long trousers
2) Destroy adult mosquitoes by indoor residual regular effective spraying
3) Preventing breeding of mosquitoes by:
- Altering the habitat to discourage breeding
- Flooding or flushing of breeding places
- Drainage to remove surface water, filling in ponds, pot holes, etc.
- Spraying breeding places with effective chemicals particularly with larvicides
4) Using drugs to:
- Prompt diagnosis and treatment of malaria cases
- Prevent infections using chemoprophylaxis, especially in nonimmune
persons visiting or going to malarious areas or in
persons with reduced immunity such as pregnant women.
5) Health education.
6) Blood screening for malaria before providing for those who need
55
 UNIT 8: CLINICAL MICROBIOLOGY

8.1 SEPTICEMIA AND BACTEREMIA

Bacteremia Septicemia
1. Bacteremia is the simple presence of Septicemia is the presence and multiplication of
bacteria in the blood. bacteria in the blood.
2. Bacteremia is not as dangerous as Septicemia is a potentially life-threatening
Septicemia. infection.
3. Less amount of bacteria are present in Large amounts of bacteria are present in the
blood. blood.
4. This may occur through a wound or It can arise from infections throughout the body,
infection, or through a surgical procedure or including infections in the lungs, abdomen, and
injection. urinary tract.
5. Toxins are not produced. Toxins may be produced by bacteria.
It shows symptoms like chills, fever,
6. Bacteremia usually causes no symptoms or
prostration, very fast respiration and/or heart
it may produce mild fever.
rate.
Untreated septicemia can quickly progress to
7. It can resolve without treatment.
sepsis.
8. Rapidly removed from the bloodstream by Antibiotics will be used to treat the bacterial
the immune system. infection that is causing septicemia.
9. Caused by Staphylococcus, Streptococcus, Staphylococci, are thought to cause more than
Pseudomonas, Haemophilus, E. coli, dental 50% of cases of sepsis. Other commonly
procedures, herpes (including herpetic implicated bacteria include Streptococcus
whitlow), urinary tract infections, peritonitis, pyogenes, Escherichia coli, Pseudomonas
Clostridium difficile colitis, intravenous drug aeruginosa, Klebsiella species and even
use, and colorectal cancer. Candida spp.

8.2. PYREXIA OF UNKNOWN ORIGIN (PUO)

Definition
It’s an increase in body temperature. Temperature greater than 38.3℃ on several occasions.
Accompanied by more than 3 weeks of illness.

56
Common causes
• Intra-abdominal abscess (liver, splenic etc)
• Bacteria, fungi and viruses
• Drug induced fever
• Wound infection
• Lung abscess
• Brain tumor
• Ulcerative colitis

Treatment
Nonsteroidal anti-inflammatory drugs (NSAIDs) and antihistamines may also be used to
treat FUOs that have no trace of underlying causes. In many people, these medications can
help reduce the fever itself. People whose fevers are thought to have an immune-deficient
origin may be treated with broad-spectrum antibiotics.

8.3. MENINGITIS
Definition
Is an inflammation (swelling) of the protective membranes covering the brain and spinal cord.

Causes of meningitis
Bacterial infections are the most common causes of meningitis.
But meningitis is also caused by viruses and fungi.

Types of meningitis
• Bacterial meningitis
• Viral meningitis
• Fungal meningitis
• Chronic meningitis

Signs and Symptoms

• High temperature.
• Cold hands and feet.
• vomiting
• confusion

57
• Breathing quickly.
• Muscle and joint pain.
• Pale skin.
• spots or a rash.

Treatment
• Most patients are given I.V. antibiotics until the laboratory findings determine the type of
meningitis, however cultures should be taken before initiating antibiotics.
• Dexamethasone or other corticosteroid is given I.V. to manage inflammation
The steroids should be used before using antibiotics.

8.4. RESPIRATORY TRACT INFECTIONS (RTI)

Definition
It’s any infectious disease of the upper or lower respiratory tract.

Clinical features
• a cough – you may bring up mucus (phlegm)
• sneezing
• a stuffy or runny nose
• a sore throat
• headaches
• muscle aches
• breathlessness, tight chest or wheezing
• a high temperature (fever)
• feeling generally unwell

Treatment
There are two types of treatments:
(i) Non - Pharmacological
-Patients should be encouraged to drink fluids that prevent dehydration and possible decrease
in in viscosity of respiratory secretions.
-Use of vaporization to promote the thinning and loosening of respiratory secretions.

(ii) Pharmacological

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-Non steroidal anti- inflammatory drugs e.g. Ibuprofen and Paracetamol.
-Antihistamines such as Diphenedrine.
-Antitussives such as Robitussin
-Steroids like Prednisone
-Antibiotics like Penicillin

8.5. DIARRHEAL DISEASES

Definitions
Diarrhoea: It is defined as passage of 3 or more loose stools per day or passing more stools
than normal for the age.
Gastroenteritis: Is an inflammation of the lining of the intestines caused by a virus, bacteria,
or parasites.
Dysentery: Is an intestinal inflammation, primarily of the colon. It can lead to mild or severe
stomach cramps and severe diarrhoea with mucus or blood in the faeces
Traveller’s diarrhoea: Is a digestive tract disorder that commonly causes loose stools and
abdominal cramps. It's caused by eating contaminated food or drinking contaminated water.

Food poisoning: Also called foodborne illness, is illness caused by eating contaminated food.
Infectious organisms — including bacteria, viruses and parasites

Classification of Diarrhoea
• Chronic
• Acute
• Watery diarrhea
• Bloody diarrhea

Causes of diarrhoea
• Infection
• Drugs
• Dietary causes
• Surgical conditions

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Symptoms of Diarrhoea
• Abdominal cramps.
• Abdominal pains.
• Urgency to go to the toilet.
• Passing of loose, watery faeces.
• Nausea.
• Vomiting.

Management of Diarrhoea:
• Replacement of the fluids
• Administration of prescribed drugs
• Maintenance of nutritional status

8.6. URINARY TRACT INFECTION (UTI)

Definition
• It is an infection in any part of urinary system- kidneys, ureters, bladder and urethra.
• It’s mostly common in women, half of all women experience a UTI in their lifetime.

Classification
• Urethritis-it’s the infection of urethra with bacteria occurs when organisms that gain access
to it colonize the periurethral glands.
• Cystitis- It’s the infection of the bladder, it’s common in females.
• Asymptomatic bacteriuria – Absence of UTI signs and symptoms are not showing
• Acute urethral syndrome- Occurs in women, is a syndrome involving dysuria, frequency
and pyuria, which resembles cystitis.
• Pyelonephritis -It’s an infection of the kidney, in women about 20% can be affected.

Signs and Symptoms

• Pain or a burning sensation when peeing (dysuria)
• Needing to pee more often than usual during the night (nocturia)
• Pee that looks cloudy.
• Needing to pee suddenly or more urgently than usual.
• Needing to pee more often than usual.
• Blood in your pee.

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Treatment
Antibiotics as prescribed by the doctor.

8.7. SEXUAL TRANSMITTED DISEASES

Definitions
STDs are infections that are spread from one person to another, usually during vaginal, anal,
and oral sex.

Types of STDs
• Chlamydia
• Gonorrhea
• Trichomoniasis
• Genital warts
• Genital herpes
• Pubic lice
• Scabies
• Syphilis, etc.

Signs and Symptoms

• Sores or bumps on the genitals or in the oral or rectal area
• Painful or burning urination
• Discharge from the penis
• Unusual or odd-smelling vaginal discharge
• Unusual vaginal bleeding
• Pain during sex
• Sore, swollen lymph nodes, particularly in the groin but sometimes more widespread
• Lower abdominal pain
• Fever
• Rash over the trunk, hands or feet

What Causes STDs?

STDs include just about every kind of infection. Bacterial STDs include chlamydia,
gonorrhoea, and syphilis. Viral STDs include HIV, genital herpes, genital warts (HPV), and
hepatitis B is caused by a parasite.

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The germs that cause STDs hide in semen, blood, vaginal secretions, and sometimes saliva.
Most of the organisms are spread by vaginal, anal, or oral sex, but some, such as those
that cause genital herpes and genital warts, may be spread through skin contact. You can get
hepatitis B by sharing personal items, such as toothbrushes or razors, with someone who has it.

Treatment
Sexually transmitted diseases (STDs) or sexually transmitted infections (STIs) caused by
bacteria are generally easier to treat. Viral infections can be managed but not always cured. If
you are pregnant and have an STI, getting treatment right away can prevent or reduce the risk
of your baby becoming infected.
Treatment for STIs usually consists of one of the following, depending on the infection:
• Antibiotics
• Antiviral drugs
8.8. HOSPITAL ACQUIRED INFECTION
Definition
It is an infection acquired in a hospital by a patient who was admitted for a reason other than
that infection.
For HAI, the infection must occur: - Up to 48 hours after hospital admission.
-Up to 3 days after discharge
-Up to 30 days after operation.

Types of HAI (by method of transmission)

• Contact transmission
- Direct contact transmission
- Indirect contact transmission
• Droplet transmission
• Common vehicle transmission
• Vector borne transmission
• Blood borne spread
• Self-infection and cross infection.

Causes
• Surgery and wound
• Intravenous procedures

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• Biomedical waste
• Lack of awareness
• Urinary bladder catheterization

Prevention and control of hospital acquired infection

• Wash Your Hands.
• Create an Infection-Control Policy
• Identify Contagions ASAP
• Provide Infection Control Education
• Use Gloves
• Provide Isolation-Appropriate Personal Protective Equipment
• Disinfect and Keep Surfaces Clean
• Prevent Patients from Walking Barefoot
• Change Linens When Daily and When Dirty.
• Make Sure Foods Are Kept at Proper Temperatures

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REFERENCES

Brown HW and Neva FA, Basic clinical parasitology, 5th ed. USA:Applenton- century
Crofts,1983.

Dey TK and Dey NC, Medical Parasitology, 9th ed. Calcutta: Allied Agency, 1984.

Nagoba, B.S., & Pichare, A. (2016). Medical Microbiology and Parasitology: Prep Manual for
Undergraduates, 3rd ed. RELX India Private Limited.

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