NJALA UNIVERSITY

COLLEGE OF MEDICAL SCIENCES - BO CAMPUS

School of Nursing

SECOND YEAR “CLASS A” - 2024/2025

LECTURE NOTE

MODULE: INTRODUCTION MICROBIOLOGY - BSNT-215

PROGRAMME: BACHELOR OF SCIENCE WITH HONOURS IN NURSING

Prepared by: Mr. Emmanuel S. Nyuma

19/11/2024

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LEARNING OBJECTIVES
At the end of this course, the learners will be able to;
• Describe the evolution of Microbiology and its relevance in nursing.
• Explain the basic concepts in microbiology.
• Classify the different types of micro-organisms.
• Classify the normal flora and the different pathogens that destroy the normal flora.
• Describe the sources of infection and microbial growth and explain the transmission path
of infection.
• Describe the various methods of microbial control.
• Name the different types of immunity and hypersensitivity.

COURSE CONTENTS
• The evolution and scope of microbiology
• Classification and characteristics of micro-organisms (structure, size, etc.)
• The normal flora of the body, Pathogenicity and common diseases and methods of study
of microbes, culture, and isolation
• Sources and types of infection, factors affecting microbial growth, infection cycle, and
the body’s reaction to infection.
• Definition of immunity, types of immunity, immunization, hypersensitivity, and
autoimmunity
• Principles and methods of microbial control – sterilization, disinfection, chemotherapy
and antibiotics, pasteurization, medical and surgical asepsis, biosafety, and waste
management
control
• Practical Microbiology – Parts of a microscope and care, observation of staining
procedures, preparation, and examination of slides and smears. Identification of common
microbes under the microscope etc.

Methods of Instruction
▪ Lectures
▪ Take-home assignments
▪ In-class practical exercises,
▪ Individual/private study
▪ Group discussions

Progressive Assessment and Examination

▪ Individual assessment (10%)
▪ Test (20%)
▪ Final Exam (70%)

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INTRODUCTION
Microbiology is derived from the Greek words mīkros which means "small”; bios, "life"; and –
logos “science” Hence is the scientific study of microorganisms, those being unicellular (single
cell), multicellular (cell colony), or acellular (lacking cells).

It the study the study of microorganisms, organisms that are of microscopic dimensions. The
organisms are too small to be seen by the naked eye i.e. less than 0.1mm and these can only be
seen using a microscope.
IMPORTANCE OF MICROBIOLOGY
▪ Promotion of betterment of human health
▪ Helps to conquer infectious and fatal infections through immunization
▪ It influences the prevention and preparing safe drinking water
▪ Used in the effective disposal of sewage and waste
To a nurse
▪ Nurses learn how disease-causing organisms enter the body and their spread
▪ Enables a nurse to understand the principles of disinfection and the effects of drugs on
microorganisms
▪ The nurse learns the importance of proper collection of specimens for bacteriological
examination in the laboratory and disease prevention
▪ A nurse will understand the meaning of reports received from the laboratory
▪ The nurse will understand how sera and vaccines are used in treatment and disease
prevention, their preparations, and effects on the body

Some economic importance of microorganisms are:

➢ They produce oxygen (by photosynthesis)
➢ Microbes help break dead or dying materials (plants, animals, corpses, faces) and return
useful substances to the soil, these microbes are called decomposers
➢ They are capable of decomposing industrial waste such as oil.
➢ Microbes help farmers by fertilizing the soil through various natural cycles such as the
nitrogen cycle.
➢ They serve as food for tiny animals, large animals then eat the smaller ones. Thus,
microbes are an important link in the food chain.
➢ They live in the digestive system of humans and animals where they help in digestion
in some cases produce substances that are of value to the host. For example, the E. Coli
bacteria that live in the human intestinal tract produce vitamins K and B, which are
absorbed and used by the human body.
➢ They are essential to the production of food and drink
➢ They produce antibiotics that are used to treat diseases. For example, penicillin was
originally produced from fungus.

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 ➢ Microbes are essential in the field of genetic engineering
➢ Microorganisms cause diseases.

PATHOGENIC MICROORGANISMS
- Any microorganism causing disease is called a pathogen
- The ability of pathogens to cause disease is called virulence
- The degree of pathogenicity is called invasion
- The invasion of the body by a pathogen is called an infection
- Pathogenicity of microbes

Note: the word “Germ” is not a scientific term, microbes that cause disease are technically
and scientifically known as pathogens. Only about 3% of microbes are pathogenic, most
microbes are “non-pathogenic” 97% i.e. they do not cause diseases.

TYPES OF MICROORGANISMS INCLUDE:

▪ Bacteria ▪ Protozoa
▪ Fungi ▪ Algae
▪ Algae ▪ Viruses
These microorganisms are studied under 5 major divisions i.e.
1. Virology-study of viruses 4. Phycology-study of algae
2. Bacteriology-study of bacteria 5. Protozoology-study of protozoa
3. Mycology-study of fungi
Prokaryote vs. Eukaryote
- All cells are divided into two groups according to the presence of the nucleus.
- Cells that have well-defined nucleus are called EUKARYOTES
- Cells that lack a nucleus are called PROKARYOTES
- All bacteria are prokaryotic organisms.

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 - Eukaryotic organisms include fungi, protozoa, helminthes, plants, animals, as well as
humans.
Prokaryotic cell
➢ Has no nucleus.
➢ Has a single, circular chromosome.
➢ The nuclear body is called the nucleoid.
➢ There is no nuclear membrane.
➢ There is no nucleolus.
➢ The cells divide by binary fission.
Eukaryotic cell
➢ Has a nucleus.
➢ Has one or more paired, linear chromosomes.
➢ The nuclear body is called the nucleus.
➢ The nucleus is bounded by a nuclear membrane.
➢ Nucleolus is present.
➢ The cell divides by mitosis.

CLASSIFICATION OF MICROORGANISMS
1. Prokaryotic microorganisms’ e.g. bacteria
These are small unicellular organisms with no defined nucleus and cell membrane
2. Eukaryotic microorganisms’ e.g. protozoa, algae, fungi, plants, and animals
These have a defined nucleus enclosing their genetic material and a cell membrane
enclosing other cell organelles
Essential characteristics of microorganisms
Characteristics Viruses Bacteria Fungi Protozoa &Helminthes
Cell No Yes Yes Yes
Type of cell None Prokaryotic Eukaryotic Eukaryotic
Diameter 0.02-0.2 1-5 3-10 15-25
Nucleic DNA or RNA DNA &RNA DNA &RNA DNA &RNA
Ribosomes Absent Present Present Present
Mitochondria Absent Absent Present Present
Nature of outside Protein capsid Rigid wall Rigid wall Flexible membrane
surface and lipoprotein containing containing
envelop peptidoglycan chitin
Motility None Some None Most
Method of replication Not binary Binary fission Budding or Mitosis
fission mitosis

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DEFINITION OF TERMS
AETIOLOGY: Is the study of the causation or origination of disease, the factors which produce
or predispose toward a certain disease or disorder.
PATHOGENECITY: The ability of a microorganism to cause disease
PATHOGENESIS: The mode of infection and process of disease causation
PATHOLOGY: The scientific study of the nature of disease and its causes, processes,
development, and consequences
EPIDEMIOLOGY: Study of a particular disease why it occurs, how it spreads among a group of
people, and what can be done to prevent it and improve the health of the community
ENDEMIC: Constant presence of a disease or agent of a disease in a community or region
EPIDEMIC: An acute outbreak of disease
OR an epidemic is the rapid spread of a disease to a large number of hosts in a given population
within a short period of time
Many endemic diseases can rapidly become epidemic if the environment or host influences change
in a way that favors transmission i.e., they start to exist in excess of normal expectans
PANDEMIC: A disease that spreads to several countries and affects a large number of people e.g.
cholera, influenza.
CONTROL: Is the suppression of infection in a community by vaccination, health education,
treatment, and sanitation
SYMBIOSIS: Is a close and often long-term interaction between different biological species e.g.
the enteric bacteria that form part of the normal flora of the GIT assist in the synthesis of vitamin
K and some of the vitamin B complex
PARASITOSIS: Infestation or infection with the parasite
COMMENSALISM: A relation between individuals of two species in which one species obtains
food or other benefits from the other without either harming or benefiting the latter e.g. numerous
birds feed on the insects turned up by grazing mammals. (This kind of relation can be contrasted
with mutualism, in which both species benefit, parasitism is an association where one organisms
benefits and another is harmed)
HOST: Is an organism that harbors a parasite (that is, a virus, a bacterium, a protozoan, or a
fungus), or a mutual or commensal, symbiont, typically providing nourishment and shelter.
A HOST CELL: is a living cell in which a virus reproduces.
A PRIMARY HOST or definitive host: is a host in which the parasite reaches maturity and, if
applicable, reproduces sexually.
A SECONDARY HOST or intermediate host: is a host that harbors the parasite only for a short
transition period, during which (usually) some developmental stage is completed. For
trypanosomes, strictly, humans are the secondary host, while the tsetse fly is the primary host,
given that it has been shown that reproduction occurs in the insect
ANAEOBES: Organisms that grow in the absence of free oxygen
OBLIGATE OR STRICT ANAEROBES are those that grow only in the absence of oxygen
FACULTATIVE ANAEROBES: These can grow either with or without free oxygen

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MICRO-AEROPHILES: theses can grow best in the presence of low amounts of oxygen
AEROBES: Organisms able to live and reproduce only in the presence of free oxygen (e.g., certain
bacteria and certain yeasts)
OPPORTUNISTS: Organisms if a suitable opportunity arises become pathogens and cause
disease normally by transfer of commensals from a usual place to another part of the body where
it establishes itself and causes disease or when the immune system is low e.g. E. coli, a normal
flora in the GIT but if it enters the urinary system, it causes UTI.

AN IMAGE OF A MICROSCOPE

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HISTORICAL DEVELOPMENT IN MICROBIOLOGY
The historical development of MICROBIOLOGY can be categorized under four era’s
1. Discovery Era
2. Transition Era
3. Golden Era
4. Modern Era

DISCOVERY ERA: “Spontaneous generation”

▪ Aristotle (384-322) and others believed that living organisms could develop from non-
living materials. (i.e. Abiogenesis)
▪ In the 13th century, Rogen Bacon described that the disease is caused by a minute “seed”
or “germ”. (i.e. biogenesis)
i. Antony Van Leeuwenhoek (1632 – 1723)
- Descriptions of Protozoa, basic types of bacteria, yeasts, and algae.
- Father of Bacteriology and protozoology.
- In 1676, he observed and described microorganisms such as bacteria and protozoa
as “Animalcules”.
- The term microbe was used by Sedillot in 1878

TRANSITION ERA
i. Francesco Redi (1626 - 1697)
- He showed that maggots would not arise from decaying meat when it is covered.
ii. John Needham (1713 – 1781)
- Supporter of the spontaneous generation theory.
- He proposed that tiny organisms (animalcules) arose spontaneously on the mutton
gravy.
- He covered the flasks with cork as done by Redi, Still the microbes appeared on
the mutton broth.
iii. Lazzaro spallanzai (1729 – 1799)
- He demonstrated that air carried germs to the culture medium.
- He showed that boiled broth would not give rise to microscopic forms of life.

GOLDEN ERA:
i. Louis Pasteur
- He is the father of Medical Microbiology.
- He pointed out that no growth took place in swan neck shaped tubes because dust
and germs had been trapped on the walls of the curved necks but if the necks were
broken off so that dust fell directly down into the flask, microbial growth
commenced immediately.

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 - Pasteur in 1897 suggested that mild heating at 62.8°C (145°F) for 30 minutes rather
than boiling was enough to destroy the undesirable organisms without ruining the
taste of the product, the process was called Pasteurization.
- He invented the processes of pasteurization, fermentation, and the development of
effective vaccines (rabies and anthrax).
- Pasteur demonstrated diseases of silkworms were due to a protozoan parasite.
- He coined the term “microbiology”, aerobic, anaerobic.
- He disproved the theory of spontaneous germination.
- He demonstrated that anthrax was caused by bacteria and also produced a vaccine
for the disease.
- He developed a live attenuated vaccine for the disease.
ii. John Tyndall (1820 - 1893)
- He discovered a highly resistant bacterial structure, later known as an endospore.
- Prolonged boiling or intermittent heating was necessary to kill these spores, and to
make the infusion completely sterilized, a process known as Tyndallisation.
iii. Lord Joseph Lister (1827-1912)
- He is the father of antiseptic surgery.
- Lister concluded that wound infections too were due to microorganisms.
- He also devised a method to destroy microorganisms in the operation theatre by
spraying a fine mist of carbolic acid into the air
iv. Robert Koch (1893-1910)
- He demonstrated the role of bacteria in causing disease.
- He perfected the technique of isolating bacteria in pure culture.
- Robert Koch used gelatin to prepare solid media, but it was not ideal because;
• Since gelatin is a protein, it is digested by many bacteria capable of producing
a proteolytic exoenzyme gelatinase that hydrolyses the protein to amino acids.
• It melts when the temperature rises above 25°C

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BACTERIOLOGY
Bacteriology is the branch of microbiology concerned with the study of bacteria. This branch is
further divided into a number of specializations that include marine bacteriology, sanitary
bacteriology, industrial bacteriology, agricultural bacteriology, and systematic bacteriology
among others.

Here, this branch of microbiology focuses on such aspects as types of bacteria and their
characteristics, diseases, and applications among others.

The Morphology and Fine Structure of Bacteria

Bacterial cells are between 0.3 and 5 lm in size. They have three basic forms: cocci, straight rods,
and curved or spiral rods. The nucleoid consists of a very thin, long, circular DNA molecular
double strand that is not surrounded by a membrane. The membrane is surrounded by the cell wall.

Bacterial Forms
Bacteria differ from other single-cell microorganisms in both their cell structure and size, which
varies from 0.3–5 lm. Magnifications of 500–1000! — close to the resolution limits of light
microscopy—are required to obtain useful images of bacteria.

BACTERIA

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Characteristics of Bacteria
▪ Bacteria are unicellular (single-celled) microorganisms.
▪ All bacteria are prokaryotes, this means they lack membrane defined nucleus, only they
have coiled single circular chromosomes.
▪ Typical bacterial cell has a rigid cell wall made of peptidoglycan (except Mycoplasma).

This cell wall is responsible for the shape of the bacterial cells and their staining properties.

The Structure of Bacteria

Bacteria structures are considered at 3 levels, namely:
i. Cell envelops proper – which contains the cell wall and cell membrane
ii. Cellular elements – enclosed within the envelope which includes, mesosomes,
ribosomes, nuclear apparatus, polyamines, and cytoplasmic granules
iii. Cellular elements that are external to the cell envelop which include flagellum,
pilus

General Properties of Bacterial

- Bacteria cells are typically prokaryotic cell
- They contain both DNA &RNA
- Most bacterial grows in artificial media
- They replicate by binary fission
- Almost all bacteria have a rigid cell wall
- They are sensitive to antimicrobial agents

Bacterial Cell Structure

Cell envelope/ Capsule:
A thick layer of viscous material is usually a polysaccharide formed by many bacteria
outside the cell wall. Some bacteria have only a thin loose layer called slime layer.
Functions of the capsule:
- Allow bacteria to adhere to the surface of host cells.
- Protect bacteria from antibodies.
- protect bacteria from phagocytosis

Cell wall:
Thick rigid layer composed mainly of peptidoglycan.
The cell wall is responsible for:
- Shape of bacterial cell (spherical, rod-like, or spiral)
- Reaction to gram stain (positive or negative)
- Bacterial cell protection from differences in osmotic pressure between the inside and outside
environment

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 Plasma membrane:
Also called cytoplasmic membrane
It is a thin membrane that encloses the cytoplasm and is made of phospholipid bilayer and
proteins.
The main function is:
- Selective permeability barrier which determines what enters and leaves the cell.
- energy production, peptidoglycan synthesis
- phospholipid synthesis
- waste removal
- Endospore formation

Cellular elements
Example:
Cytoplasm:
Cytoplasm is a complex fluid mixture of 80% water containing amino acids, lipids,
carbohydrates, ions, and enzymes. Nucleoids, ribosomes, inclusion granules, and plasmids
(cellular organelles) are suspended and embedded in this fluid.
Nucleoid:
The nucleoid (chromosome) of the bacterial (prokaryotic) cell is the equivalent of the
nucleus of the eukaryotic cell. There is no nuclear membrane but a long coiled and
supercoiled single circle of Deoxyribo-Nucleic Acid DNA.

Cellular elements that are external to the cell envelop

Flagella:
Flagella are long hollow tubular filaments that enable bacteria to move. Bacterial cells may
have one flagellum at one pole (Monotrichous) for example Vibrio cholera, or many
flagella arranged at one pole, at both poles (Amphitrichous), or distributed over the whole
cell surface (Peritrichous).
Pili:
Pili also called fimbriae are thin hair-like appendages on the surface of many gram-negative
bacteria -- also found on very few gram-positive bacteria -- they function as adhesion
organs to attach the bacterial cell to the surface of the host cell.

Classification of bacteria
Bacteria can be classified on the following bases:
- Morphological arrangement - Biochemical reaction
- Staining - Antigenic structure
- Cultural characteristics - Composition of DNA

But medically important bacteria may be classified based on any of the following:
1. Morphology (shape)
2. Growth requirement
3. Gram staining
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Morphology of bacteria
There are 3 basic shapes of bacteria:
1. Spherical or oval in shape (cocci)
2. Rod-like (bacilli)
3. Spiral or corkscrew shape (spirilla).
- The inner structures of the bacterial cell, the cytoplasm, the nucleoid, the ribosomes,
plasmids, and the inclusion bodies are contained in the cell envelope, which is made of
three layers from inside out, the cytoplasmic membrane, the cell wall, and the capsule.
- Two surface appendages may be present, flagella which enables bacteria to move, and pili
which are used in attachment to host cells.

Bacterial cells arrangement:

Many bacterial species show characteristic arrangement depending on the plane of division of
the cell and the tendency of the cells to adhere to each other.

COCCI
Single = coccus
Double (pairs) = diplococci
Chains = streptococci Clusters = staphylococci

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BACILLI single = bacillus
Double (pairs) = diplobacilli
Chains = streptobacilli

Bacterial staining methods

As they exist in nature, bacteria and other microorganisms are colorless, transparent, and difficult
to see. So stains enable us to observe the morphology, and size and differentiate between one group
of bacteria from the other.

Therefore, various staining methods have been developed to enable scientists to examine them.
Bacterial staining is the process of coloring bacteria's structural components using stains and dyes.
The purpose of staining is to; identify microorganisms selectively by using dyes, fluorescence, and
radioisotope emission

The general methods of staining are; Direct and Indirect staining methods.
Direct staining method – is the process by which microorganisms are stained with simple dyes.
Example methylene blue
Indirect stain – is the process that requires mordants (a substance that enables a particular material
to return to its original color after staining.

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Types of microbiological stains
1. Basic stains
2. Acidic stains
3. Neutral stains
Basic stains – are stains in which the coloring substance is contained in the base part of the stain.
Acidic – are stains in which the coloring substances are contained in the acidic part of the stain
Neutral – are stains in which the acidic and basic components of stains are colored.

Types of staining methods

1. Simple staining method
2. Differential staining method
3. Special staining method
Simple staining method - only a single dye is used. It is used to demonstrate bacterial morphology
and arrangement; it is of two types; positive staining in which the bacteria or its part is stained by
a dye and negative staining in which the dye stains the background, but the bacteria itself remains
unstained.
Differential staining - in this method, multiple stains are used to differentiate different cell
structures and cell types.

GRAM STAIN:
Gram staining is the most useful procedure in diagnostic microbiology, commonly used to identify
unknown bacteria. It classifies bacteria into two groups, that is: Gram-positive (stains purple or
violet) and Gram-negative (stains pink or red).
Gram Positive staining (Gram-positive bacteria stain blue-violet)
Gram Negative staining (Gram-negative bacteria stain red)

Procedure:
1. Prepare a smear and heat-fix it.
2. Apply crystal violet solution (leave it for one minute).
3. Wash the slide with water.
4. Apply iodine solution (leave it for one minute).
At this time all bacteria appear violet (same color), that is, simple staining.
5. Wash the slide with water.
6. Decolorize with acetone (for 5 seconds only).
7. Now gram-positive bacteria are still visible (violet-colored) but gram-negative
bacteria are no longer visible.
8. Wash immediately in water.
9. Apply safranin (the counter stain) (for 30 seconds).
10. Wash the slide with water.
11. Blot and dry in the air.

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Now on examination under microscope types of bacteria are visible, the Gram-positive bacteria
appear purple or violet and the Gram-negative bacteria appear pink or red.

Gram-Negative Bacteria Examples:

There are many groups of Gram-Negative bacteria such as Cyanobacteria, Spirochaetes, and
Proteobacteria etc. Out of which, proteobacteria is one of the major groups of known Gram-
Negative bacteria (it includes bacteria like E-coli, Salmonella, Pseudomonas, Moraxella,
Helicobacter, Stenotrophomonas, Legionella, Acetic Acid Bacteria, etc.).
Neisseria gonorrhea or N meningitidis

Bacterial Growth
Bacterial reproduction:
- Bacterial reproduction is by binary fission. This means that each cell grows and splits into
two cells.
- Generation time is the period in which bacteria divide, and each cell becomes two cells.
In other words, it is the period needed to double the number of cells (doubling time).
- This period is different from one species to another, and it can be as short as twenty minutes
(20 min.) or as long as several days.

Bacterial growth curve:

Growth of bacteria goes through four (4) phases, that is: lag phase, log phase, stationary phase,
and decline (death) phase.

Bacterial growth curve

1 - LAG phase
The lag phase is a period of adjustment after the bacteria enter the body of a host or culture
media.
- The bacteria are adjusting to the environment.
- Cells are active and there is an increase in cell size. They synthesize the components
needed for cell division.
- Little or no cell division is occurring.

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2 - LOG phase
The number of cells increases exponentially at a constant rate (the doubling time).
BECAUSE
- Bacteria has adjusted to the environment
- Reproduction is taking place

3 - STATIONARY phase
During this phase, the number of viable cells remains constant. The growth rate equals the
death rate. Decreased growth rate and death is due to:
- Depletion of nutrients.
- Accumulation of waste products.
- Change in pH.
4 - DEATH phase
In the decline (death) phase the death rate is more than the growth rate that is, more bacteria
die. The number of viable cells decreases.

Characteristics of some clinically important bacteria

Gram-positive bacteria
Gram-positive bacteria Associated diseases
Bacillus anthracis Anthrax
Cyanobacterium Diptheriae Diphtheria
Streptococcus Aureaus Skin infections, Cellulitis, Osteomyelitis,
Pneumonia, Nosocomial infections
Clostridia Clostridium tetanii (tetanus), Clostridium
perfrigens (gas gangrene), Clostridium
batulinium (food poisoning)
Bordetella Pertusis Pertussis (whooping cough)
Gram Negative Bacteria
Gram Negative Bacteria Associated diseases
Escherichia Coli URTIs, Gastro-enteritius, E-coli associated
with diarrhoea
Pseudomonas Aureginosa URTI’s, Pneumonia, Burn infection
Salmonella Typhoid fever (enteric fever), Enterocolitis
Vibrio Cholera Cholera
Mycobacterium Tuberculosis Tuberculosis
Treponema Pallidum syphilis

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VIROLOGY (Study of viruses)
Viruses are about a hundred times smaller than human cells and many times smaller than bacteria
and fungi. The discipline of microbiology that is concerned with the study of viruses is known as
virology and scientists who make virology their field of study are known as virologists.

Characteristics Of Virus
Size 25nm (picornavirus) to 250 x 350nm (smallpox virus). Resolving power of a
light microscope: 300nm, bacteria: 500–5000nm.

Structure Viruses are complexes comprising virus-coded protein and nucleic acid; some
viral species carry cell-coded components (membranes, RNA).
Genome DNA or RNA. Double-stranded or single-stranded nucleic acid, depending on
the species

Reproduction Only in living cells. The virus supplies the information in the form of nucleic
acids and in some cases a few enzymes; the cell provides the remaining
enzymes, the protein synthesizing apparatus, the chemical building blocks,
the energy, and the structural framework for the synthetic steps.

Antibiotics Viruses are unaffected by antibiotics but can be inhibited by interferon and
certain chemotherapeutic agents.

General Characteristics of Viruses

- Virus means “poison” (Latin)
- Viruses are very small infectious agents, (20 - 300 nanometers)
- A virus is a piece of nucleic acid (Genome) surrounded by a protein coat (Capsid).
- The nucleic acid and capsid together are called Nucleocapsid

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 - In some viruses the nucleocapsid is surrounded by a lipid envelope.
- An intact completely infectious viral particle is called a virion.
- They are acellular (not made up of cells); that is, they contain no cytoplasm or cellular
organelles.
- They do not grow or divide
- They are obligate intracellular parasites, (they are unable to multiply outside the living host
cells)
- They can infect animals, plants, and even other microorganisms.
- Viruses which infect only bacteria are called Bacteriophages
- Viruses that infect only fungi are termed Mycophages

A virus simply consists of:

1 – Genome 2 – Capsid 3 – Envelope

Viral Genome (Nucleic Acid)

- The viral genome has the genes (codes) for the synthesis of viral components and viral
enzymes for replication.
- The type of nucleic acid may be: RNA or DNA (but never both).
Capsid
- The capsid is a protein shell surrounding the genome
- The capsid serves to:
a. Protect the viral genome.
b. Introduce the viral genome into host cells.
- The shape of the capsid may be:
a. Icosahedral symmetry (spherical)
b. Helical symmetry (rod-shaped or coiled)
c. Complex symmetry irregular shape (neither helical nor polyhedral)

Complex Icosahedral Helical

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Envelope
- Some viruses have an additional covering, called the envelope.
- The envelope is a lipid bilayer containing proteins
- It is derived from host cell membranes, however, its proteins are replaced by virus-specific
proteins

There are 5 major steps in the replication cycle of all viruses:

1. Adsorption (Attachment)
2. Penetration
3. Nucleic acid and protein synthesis
4. Assembly of virions
5. Release (Egress)

1 - Adsorption (Attachment)
- Adsorption or attachment is the binding of the virus to the surface of the host cell
- Specific proteins on the surface of the virion bind to special receptors on the host cell
2 - Penetration
- Entry of the virus genome into the host cell
3 - Nucleic acid and protein synthesis
- This involves
- Synthesis of viral proteins,
- Replication of the viral nucleic acid
4 - Assembly of virions
- Assembly means combining viral nucleic acid with viral capsid
- For enveloped viruses, it involves also the acquisition of an envelope
- Some viruses assemble in the cytoplasm, others assemble in the nucleus
5 - Release (Egress)
- This may occur by:
- Disintegration or lysis of the infected cell which results in the release of intact infectious
virions

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Characteristics of some clinically important viruses
Virus Associated disease
- Acute febrile pharyngitis
Adenovirus - Viral pneumonia
- Follicular conjunctivitis
- Keratoconjunctivitis
- Infantile gastroenteritis
Poliovirus - Poliomyelitis
Hepatitis A virus - Hepatitis A (Infectious hepatitis)
Hepatitis B virus - Hepatitis B
- Primary hepatocellular carcinoma
(HCC; hepatoma)
Hepatitis C virus - Hepatitis C
Human Immunodeficiency Virus (HIV) - Acquired Immunodeficiency
Syndrome (AIDS)
Rotavirus - Gastroenteritis
Herpes simplex virus, type 1 - Gingivostomatitis
- Keratitis
Influenza virus - Influenza (flu)
Measles virus - Measles
Rabies virus - Rabies
Herpes Zoster virus - VZV
Corona virus - Covid-19
Ebola virus EVD

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MYCOLOGY (Study of fungi)
Fungi are eukaryotic microorganisms (domain eucarya) that occur ubiquitously in nature. Only
about 200 of the thousands of species have been identified as human pathogens, and among these
known pathogenic species fewer than a dozen are responsible for more than 90% of all human
fungal infections.

The fungi (Mycota) kingdom comprises over 50,000 different species, but only about 200 have
been identified as human pathogens. Only about a dozen of these “pathogenic” species cause 90%
of all human mycoses.

General characteristics of pathogenic fungi

- Fungi are eukaryotes
- Fungal cells have a rigid cell wall composed mainly of chitin (polysaccharide).
- They are nonmotile
- They are heterotrophs (require organic carbon source for growth).

Morphology of pathogenic fungi

Pathogenic fungi of medical importance occur in two main shapes:
1. Yeast
- Unicellular (single-celled)
- Round to oval in shape
- Size: 5 - 25 pm in diameter
2. Mould (Mold)
- Multicellular
- Long filaments (tube-like) known as hyphae (singular = hypha)
- Size of hyphae cell: 2 - 5 pm in width and 5 - 50 pm in length
3. Dimorphic fungi
Are those fungi which grow in either form (yeast-like and mold like) under different environmental
conditions, for example, temperature.

Yeast Mold Dimorphic

- 22 -

Growth reproduction
Fungi may reproduce asexually, sexually or both ways.
Sexual spores: result from the fusion of nuclei from two cells. Fusion of two haploid nuclei forming
diploid and then division by meiosis (reduction division) producing sexual spores (Ascospores).

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MYCOSES
Fungal diseases (Mycoses) are classified by the location of the infection
1. Superficial (cutaneous) mycoses:
Organisms responsible for cutaneous mycoses are called dermatophytes Infections are
limited to outer layers of skin, hair, and nails Some of the cutaneous mycoses include
Pityriasis versicolor (Malassezia furfur), Tinea cruris, T. corporis, & Tinea unguium
(Microsporum sp, Trichophyton sp. & Epidermophyton sp).
2. Subcutaneous mycoses:
Infections involving the dermis, subcutaneous tissues, muscle, fascia, and bone.

Usually result from puncture wounds and often form disfiguring Subcutaneous abscesses
e.g. Chromomycosi (Cladosporium carionii), & Madura foot (Madurella grisea)
3. Systemic mycoses:
Fungal infections of the internal organs
Infections originate primarily in the lungs and may spread to many organ systems
Organisms responsible for systemic mycoses are true pathogens (can infect normal
healthy individuals)

Conditions include Histoplasmosis (Histoplasma capsulatum), Coccidioidomycosis

(Coccidioides immitis), & Blastomycosis (Blastomyces dermatitidis).
4. Opportunistic mycoses:
Usually don’t occur in healthy people Occur in Immuno-compromised persons
May result from un-careful and random use of broad-spectrum antibiotics Conditions
include Candidiasis (Candida albicans), Aspergillosis (Aspergillus fumigatus),
Cryptococcosis (Cryptococcus neoformans), Pneumonia (Pneumocystis carinii)

23
PARASITOLOGY
Parasitology is a wide field of microbiology that deals with the study of parasites. For the most
part, parasitology is concerned with organisms found in three major groups including protozoa,
helminths (worms), and arthropods.
Given that parasitology is concerned with disease-causing organisms (as well as vectors) it has
been influenced by a number of other disciplines including immunology and biochemistry among
others. Like mycology and phycology, parasitology entails the study of both unicellular and
multicellular organisms. Those who study parasitology are known as parasitologists.

Parasite - a living organism that lives in (endoparasite) or on (ectoparasite) another organism,

termed its host. It obtains nourishment and protection while offering no benefit in return.
Consequently, the host suffers from various diseases, infections, and discomforts.
However, in some cases, the host may show no signs at all of infection by the parasite.
The three main branches of parasitology are:
- Protozoan (parasitic protozoan – mostly ectoparasites and endoparasites)
- Helminthes (parasitic metazoans - endoparasites)
- Arthropods (Parasitic arthropods- ectoparasites)
Types of Parasites
According to the nature of the host-parasite interactions and the environmental factors, the
parasite may be one of the following types:
▪ An obligatory parasite: these are parasites that are completely dependent on their host
and can’t survive without them during part or all of their life cycle e.g. Plasmodium
▪ A facultative parasite: that can change its lifestyle between non-parasitic in the
environment and parasitic according to the surrounding conditions. Not dependent on
parasitism but can adapt to it.
▪ An accidental parasite: that affects an unusual host e.g. Toxocara canis (a dog parasite)
in man.
▪ A temporary parasite: that visits the host only for feeding and then leaves it. E.g. Bed
bug visiting man for a blood meal.
▪ A permanent parasite: that lives in or on its host without leaving it e.g. Lice.
▪ An opportunistic parasite: that is capable of producing disease in an immune-deficient
host (like AIDS and cancer patients). In the immuno-competent host, it is either found
in a latent form or causes a self-limiting disease e.g. Toxoplasma gondii.
▪ A zoonotic parasite: that primarily infects animals and is transmittable to humans. e.g.
anthrax, Fasciola species etc.

Types of Hosts
Hosts are classified according to their role in the life cycle of the parasite into:

24
 ▪ Definitive host (DH) - that harbours the adult or sexually mature stages of the parasite
(or in whom sexual reproduction occurs) e.g. man is DH for Schistosomiasis, while
female Anopheles mosquito is DH for Plasmodium species (malaria parasites).
▪ Intermediate host (IH) - those harbours larval or sexually immature stages of the
parasite (or in whom asexual reproduction occurs) e.g. man is IH of malaria parasites.
▪ Reservoir host (RH) - Harbours the same species and same stages of the parasite as
man. It maintains the life cycle of the parasite in nature and is, therefore, a reservoir
source of infection for man. e.g. sheep are RH for Fasciola hepatica.
▪ Paratenic or transport host- Serves as a temporary refuge and vehicle for reaching an
obligatory host, usually the definitive host. Paratenic hosts bridge the gap between the
intermediate and definitive hosts. For example, dogs and pigs may carry hookworm
eggs from one place to another, but the eggs do not hatch or pass through any
development in these animals.

Classification and General Characters of Human Parasites

The classification of parasites is controversial as there is no universally accepted system.
Parasites form part of the animal kingdom which comprises about 800,000 identified species
categorized into 33 phyla.
The most acceptable taxonomic classification of human parasites includes Endoparasites and
Ectoparasites.
ENDOPARASITES - are sub-classified into Helminthic parasites (multicellular organisms)
and Protozoan parasites (unicellular organisms). Helminthic parasites are either flat worms
(Trematodes), segmented ribbon-like worms (Cestodes), or cylindrical worms (Nematodes).
Most parasites of humans live inside the host (endo- means internal). These are helminthes
(worms of various types), protozoa, or sometimes larval stages of arthropods (insects, mites)
Both helminthic and protozoan parasites can infect different tissues and organs of the human
body. A great number of endoparasites live in the intestines, or at least pass through the
intestines, having been swallowed in food or water. Virtually any organ can be affected,
however, some parasites like Trichinella and Toxoplasma gondii live in muscles, larvae of and
liver flukes occupy the liver, Schistosoma hematobium targets the urinary bladder and most of
the protozoan parasites circulate in the blood.
ECTOPARASITES - Human ectoparasites live on the host (ecto- means outside of). They
include fleas, lice, mosquitoes, bugs, mites, ticks, etc. In general, ectoparasites attach to the
skin to feed and do not remain on the host for their entire lives.
Common Name Latin Name Part of the body
1. Tick, Mites Arachnida Skin
2. Lice (insect) Pediculi Hair follicles
3. Bugs (insect) Heteroptera Skin
4. Mosquitoes/flies(insect)
5. Fleas (insect) Sphronatera

25
PROTOZOOLOGY
It is the sub-discipline that deals with the study of protozoa. Like fungi, these are eukaryotic
organisms that include groups such as amoeboids, ciliates, sporozoans, and flagellates. Given that
a good number of these organisms have been associated with animal and human diseases,
protozoologists not only focus on their taxonomy and morphological aspects for classification
purposes but also for medical significance.

Some common examples of diseases caused by protozoa include malaria, sleeping sickness as well
as amoebic dysentery.

General Characteristics of Protozoa

- The protozoa are unicellular organisms
- They are eukaryotic organisms
- They are heterotrophs
- The vegetative, reproducing, feeding form of a protozoan is called a "trophozoite"
- Some protozoa produce a protective, hardened capsule called a "cyst"

Pathogenic protozoa are divided into four groups based on their means of motility:
1. Amoebas
2. Flagellates
3. Ciliates
4. Protozoa

HELMINTHS
General Characteristics of Helminths
- The helminths are parasitic worms
- They are multicellular eukaryotic organisms
- They generally possess digestive, circulatory, nervous, excretory, and reproductive
systems
- There are three groups of helminths:
1. Trematodes (flukes)
2. Cestodes (tapeworms)
3. Nematodes (roundworms)

26
 Medically important Protozoan and helminthes
A. Protozoan
Common Name Latin Name Parts Of the Body
1. Amoebiosis Entamoeba hastolytica Mainly large intestine
2. Giardiasis Giardia lamblia Mainly small intestine
3. Malaria Plasmodium: falciparum, vivax, ovale, Red blood cell
malariae & knowlesi
4. Trichomoniasis Trichomonas vaginalis Female U-Tract
5. Sleeping sickness Trypanosoma brucei
B. Helminthes (Worm)
1. Flatworms/Tape - Taenia saginata (Beef) Intestines
Worms - Taenia solium (Pork) Brain, eye & muscles
(Cestoda) - Enhinococcus granulosus Liver, lungs, kidneys
- Taenia multicep Intestines
2. Fluke
(Trematoda)
I. Liver fluke - Faciola hepatica Liver& gall bladder
II. Blood flukes - Schistosoma mansoni (intestines) Intestines, Liver &
(schistosomiais) - Schistosoma haematobium (Urinary) kidney, bladder and
- Schistosoma japonicum ureter
3. Roundworm Intestinal Nematades
(Nematoda) - Ancylostoma duodenale (hookworm) Lungs, small intestine,
- Ascaris lumbricoides (Large roundworn) blood
- Necator americanus Intestines, liver, lung,
- Stronyloids pancrease &
- Trichuris trichiara (wipe worm) appendix
- Enterobius vermiculus (pinwrorm) Large intestine
Intestines
Other medically important helminths
Guinea worm Tissues and vascular nematodes Tissues and muscles
Dracunculus medinensis
Filarioidae
River blindness Onchocerca volvulus Eye
Trichinella
Elephantiasis Wuchereria bancrofti Lymphatic system

27
PHYCOLOGY
Phycology is one of the branches of microbiology that is concerned with the study of multicellular
organisms. Unlike mycology, however, phycology deals with the study of different types of algae
that can be found in different types of environments.

While they may exist as small microorganisms found floating in the ocean, some algae grow to
form large seaweeds found in the aquatic environments. Apart from being part of the food chain,
algae are also involved in the production of oxygen which makes them important in microbiology.
Those who study phycology (e.g. Carl Adolph Agardh) are known as phycologists.

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NORMAL FLORA
Normal floras are organisms that inhabit the body of a healthy person without causing disease
under normal circumstances. They are usually bacteria or yeast, viruses, protozoa, and worms are
not considered to be the normal flora.

Normal flora are non-pathogenic, especially in their usual anatomic sites but may cause disease
when they move to another site, especially in immunosuppressed patients and such diseases are
referred to as opportunistic infections.

Types of normal flora

- Resident flora: they are commonly found in a particular area of the body at a given age
- Transient flora: are microorganisms that are present at a given time and disappear or die
off within hours, days, weeks or months.

The Most Important Microorganisms of the Normal Flora with their Localizations.
Normal Flora
Skin OC GIT URT GT
Staphylococci +++ + + ++ ++
Enterococci ++
a-hemolytic streptococci + +++ + + +
Anaerobic cocci + +
Pneumococci + +
Apathogenic neisseriae + + +
Apathogenic corynebacteria ++ + + + +
Aerobic spore-forming bacteria (+)
Clostridia +++ +
Actinomycetes +++
Enterobacteriaceae + + +++ + +
Pseudomonas +
Haemophilus + ++ +
Gram-neg. anaerobes +++ +++ +++ +++
Spirochetes ++ + +
Mycoplasmas ++ + + ++
Fungi (yeast) ++ + + + +
Entamoeba, Giardia, Trichomonas + +

Note: +++ = numerous, ++ = frequent, + = moderately frequent, (+) = occasional occurrence

OC: oral cavity, GIT: gastrointestinal tract, URT: upper respiratory tract, GT: genital tract

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Benefits of Normal Flora to the Host
- Prevents colonization by pathogens through competing for nutrients and receptor sites with
pathogens
- Those in the gut secrete vitamin K and B complex which supplements food sources to the
host
- Stimulates antibody mediated immune response that may cross-react with future pathogens
hence preventing diseases
- Lactobacilli in the vagina produce acids which maintain low PH hence inhibiting the
growth of microorganisms such as candida albicans
- those found in the gut produce antimicrobial substances which kill or inhibit the growth of
pathogens

What Causes Normal Floras to Become Pathogenic

- Suppression of the normal flora by antibiotics allowing overgrowth of resistant species
- Immunosuppression
- Hormonal changes especially during pregnancy and menstruation
- Introduction of microorganisms to new sites eg E. coli from the anus to the vagina leading
to UTI

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INFECTION
Infection is the successful entry and multiplication of pathogenic microorganisms in the body.
Typical stages of an infectious disease
A typical acute infectious disease has four stages:
i. Incubation period- which is the time between the acquisition of the organism (toxin)
and the beginning of symptoms.
ii. Prodromal period – during which nonspecific symptoms such as fever, malaise, and
loss of appetite occurs
iii. Specific illness period – during which the overt characteristic signs and symptoms of
the disease occur
iv. Recovery period – during which the illness abates, and the patient returns to a healthy
state
Cycle of Infection (Transmission Cycle)
The chain of infection is a set of 6 intertwined links that allow for communicable diseases to
spread. Each step of the chain is required to effectively transmit infectious illness. Breaking any
one of the 6 links can slow the spread of infectious disease.
- Prevention and control of infection is of vital importance to the patient as well as to health
care personnel.
- To provide proper care for patients with communicable diseases or infectious organisms,
you should understand the components of infection and the methods to control the cycle of
infection.
- The cycle of infection (see diagram below) is like a chain consisting of six links.
- To produce disease, each link of the infectious process must be present in a logical
sequence. Removing one link in the chain will control the cycle of infection
The six links in the chain are:
1. The Infectious Agent – or the microorganism which can cause disease.
2. The Reservoir or source of infection where the microorganism can live and thrive. This
may be a person, an animal, any object in the general environment, food or water.
3. The Portal of Exit from the reservoir. This describes the way the microorganism leaves
the reservoir. For example, in the case of a person with flu, this would include coughing
and sneezing. In the case of someone with gastro-enteritis microorganisms would be
transmitted in the faeces or vomit.
4. The Mode of Transmission. This describes how microorganisms are transmitted from one
person or place to another. This could be via someone’s hands, on an object, through the
air or bodily fluid contact.
5. The Portal of Entry. This is how the infection enters another individual. This could be
landing on a mucous membrane, being breathed in, entering via a wound, or a tube such as
a catheter.
6. The Susceptible Host. This describes the person who is vulnerable to infection.
Infection can be prevented by breaking the Chain of Infection.
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The most susceptible persons to the disease include.
1. very young Children.
2. People who are very old.
3. People on inadequate diets.
4. People who are chronically ill.
5. People receiving medical therapy.
6. People who are already ill.
7. People with open wounds.

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Sources of Infection to Man
- Insects
- Man
- Animals
- Vectors acting as reservoir hosts
- Soil
- Water
- Food
Infection Control
Infection prevention and control measures aim to ensure the protection of those who might be
vulnerable to acquiring an infection both in the general community and while receiving care due
to health problems, in a range of settings.

- The basic principle of infection prevention and control is hygiene.

- A breach in infection control practices facilitates the transmission of infection from
patients to healthcare workers, other patients, and attendants.
- It is therefore important for all healthcare workers, patients, their family members, friends,
and close contacts to adhere to the infection control guidelines strictly.
- It is also imperative for healthcare administrators to ensure the implementation of the
infection control program in healthcare facilities.
- Infection control practices can be grouped into two categories

33
 1. Standard precautions.
2. Additional (transmission-based) precautions.

Transmission of infections in health care facilities can be prevented and controlled through the
application of basic infection control precautions which can be grouped into standard
precautions, which must be applied to all patients at all times, regardless of diagnosis or infectious
status, and additional (transmission-based) precautions which are specific to modes of
transmission (airborne, droplet and contact). The terms “standard precautions” and “additional
(transmission-based) precautions” have replaced previous terms such as universal blood and body
fluid precautions, universal precautions, and barrier nursing.

Standard Precautions
Treating all patients in the health care facility with the same basic level of “standard” precautions
involves work practices that are essential to provide a high level of protection to patients, health
care workers, and visitors. These include the following:
- hand washing and antisepsis (hand hygiene).
- use of personal protective equipment when handling blood, body substances, excretions,
and secretions.
- appropriate handling of patient care equipment and soiled linen.
- prevention of needle stick/sharp injuries.
- environmental cleaning and management; and
- Appropriate handling of waste.

Hand washing and Antisepsis (hand hygiene)

Appropriate hand hygiene can minimize micro-organisms acquired on the hands during daily
duties and when there is contact with blood, body fluids, secretions, excretions, and known and
unknown contaminated equipment or surfaces.

Wash or decontaminate hands:

- after handling any blood, body fluids, secretions, excretions, and contaminated items.
- between contact with different patients.
- between tasks and procedures on the same patient to prevent cross-contamination between
different body sites.
- immediately after removing gloves; and
- Use a plain soap, or antimicrobial agent, such as an alcoholic hand rub or waterless
antiseptic agent.

The hospital setting is a good setting for communication about personal hygiene, such as informing
visitors and the general public about hygiene rules such as washing hands.

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The 5 Moments
- Moment 1 - Before touching a patient.
- Moment 2 - Before a procedure.
- Moment 3 - After a procedure or body fluid exposure risk.
- Moment 4 - After touching a patient.
- Moment 5 - After touching a patient's surroundings.

THE SEVEN STEPS IN HAND WASHING

35
Washing your hands is easy, and it’s one of the most effective ways to prevent the spread of
germs. Follow these five steps every time.
1. Wet your hands with clean, running water (warm or cold), turn off the tap, and apply
soap.
2. Lather your hands by rubbing them together with the soap. Lather the backs of your
hands, between your fingers, and under your nails.
3. Scrub your hands for at least 20 seconds. Need a timer? Hum the “Happy Birthday”
song from beginning to end twice.
4. Rinse your hands well under clean, running water.
5. Dry your hands using a clean towel or an air dryer

Use of personal protective equipment

Using personal protective equipment provides a physical barrier between microorganisms and
the wearer. It offers protection by helping to prevent micro-organisms from:
- contaminating hands, eyes, clothing, - protective eyewear (goggles).
hair, and shoes. - mask.
- being transmitted to other patients - Apron.
and staff Personal protective - gown.
equipment includes: - boots/shoe covers; and
- gloves. - Cap/hair cover.

Personal protective equipment should be used by:

- Health care workers who provide direct care to patients and who work in situations where
they may have contact with blood, body fluids, excretions, or secretions.
- support staff including medical aides, cleaners, and laundry staff in situations where they
may have contact with blood, body fluids, secretions, and excretions.
- laboratory staff, who handle patient specimens; and
- Family members who provide care to patients and are in a situation where they may have
contact with blood, body fluids, secretions, and excretions.
Principles for use of personal protective equipment
• Personal protective equipment reduces but does not eliminate the risk of acquiring an
infection.
• It is important that it is used effectively, correctly, and at all times where contact with
• blood and body fluids of patients may occur.
• Continuous availability of personal protective equipment and adequate training for its
proper use are essential. Staff must also be aware that the use of personal protective
equipment does not replace the need to follow basic infection control measures such as
hand hygiene.

36
The following principles guide the use of personal protective equipment:
- Personal protective equipment should be chosen according to the risk of exposure. The
healthcare worker should assess whether they are at risk of exposure to blood, body
fluids, excretions, or secretions and choose their items of personal protective equipment
according to this risk.
- Avoid any contact between contaminated (used) personal protective equipment and
surfaces, clothing, or people outside the patient care area.
- Discard the used personal protective equipment in appropriate disposal bags, and dispose
of it as per the policy of the hospital.
- Do not share personal protective equipment.
- Change personal protective equipment completely and thoroughly wash hands each time
you leave a patient to attend to another patient or another duty.
Prevention of needle stick/sharps injuries
- Take care to prevent injuries when using needles, scalpels, and other sharp instruments or
equipment.
- Place used disposable syringes and needles, scalpel blades, and other sharp items in a
puncture-resistant container with a lid that closes and is located close to the area in which
the item is used.
- Take extra care when cleaning sharp reusable instruments or equipment.
- Never recap or bend needles.
NB: Sharps must be appropriately disinfected and/or destroyed as per the national standards
or guidelines.

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Environmental Management Practices
A clean environment plays an important role in the prevention of hospital associated infections
(HAI). Many factors, including the design of patient care areas, operating rooms, air quality,
water supply, and laundry, can significantly influence the transmission of HAI.

Premises/buildings
Facility design and planning should ensure:
• adequate safe water supply. • regulation of traffic flow to minimize
• appropriate cleaning practices exposure of high-risk patients and
• adequate floor space for beds. facilitate patient transport.
• adequate inter-bed space • measures to prevent exposure of
• adequate hand washing facilities. patients to fungal spores during
• Adequate ventilation for isolation renovations.
rooms and high-risk areas like • precautions to control rodents, pests,
operation theatres, transplant units, and other vectors; and
intensive care areas, etc. • Appropriate waste management
• adequate isolation facilities for facilities and practices.
airborne, droplet, contact isolation,
and protective environments.

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Air (Ventilation)
Ventilation systems should be designed and maintained to minimize microbial contamination. The
air conditioning filters should be cleaned periodically and fans that can spread airborne pathogens
should be avoided in high-risk areas.

Water
The health care facility should provide safe water. If it has water storage tanks, they should be
cleaned regularly, and the quality of water should be sampled periodically to check for bacterial
contamination.

Safe drinking water

- Where safe water is not available, boil water for 5 minutes to render it safe
- Alternatively, use water purification units.
- Store water in a hygienic environment
- Do not allow hands to enter the storage container.

Cleaning of the hospital environment

Routine cleaning is important to ensure a clean and dust-free hospital environment. There are
usually many micro-organisms present in “visible dirt”, and routine cleaning helps to eliminate
this dirt. Administrative and office areas with no patient contact require normal domestic cleaning.
Most patient care areas should be cleaned by wet mopping. Dry sweeping is not recommended.
The use of a neutral detergent solution improves the quality of cleaning. Hot water (80°C) is a
useful and effective environmental cleaner. Any areas visibly contaminated with blood or body
fluids should be cleaned immediately with detergent and water.

Isolation rooms and other areas that have patients with known transmissible infectious diseases
should be cleaned with a detergent/ disinfectant solution at least daily. All horizontal surfaces and
all toilet areas should be cleaned daily.

Hospital Waste
Hospital waste can also be known as medical waste or clinical waste. Specifically, clinical waste
is any waste that poses a risk of contamination or infection.

Hospital waste is essentially categorized in two different ways: whether it is hazardous or non-
hazardous.

Types of waste
Waste and by-products cover a diverse range of materials, including:
• infectious waste: waste known or suspected to contain pathogens and pose a risk of disease
transmission, e.g. waste and wastewater contaminated with blood and other body fluids,

39
 including highly infectious waste such as laboratory cultures and microbiological stocks;
and waste including excreta and other materials that have been in contact with patients
infected with highly infectious diseases in isolation wards.
• pathological waste: human tissues, organs or fluids, body parts, foetuses, unused blood
products, and contaminated animal carcasses.
• sharps waste: used or unused sharps, e.g. hypodermic, intravenous or other needles; auto-
disable syringes; syringes with attached needles; infusion sets; scalpels; pipettes; knives;
blades; broken glass;
• chemical waste: for example, solvents and reagents used for laboratory preparations,
disinfectants, sterilants, and heavy metals contained in medical devices (e.g. mercury in
broken thermometers) and batteries.
• pharmaceutical and cytotoxic waste: pharmaceuticals that are expired or no longer
needed; items contaminated by, or containing, pharmaceuticals. Cytotoxic waste
containing substances with genotoxic properties, e.g. waste containing cytostatic drugs
(often used in cancer therapy), genotoxic chemicals.
• radioactive waste: such as products contaminated by radionuclides including radioactive
diagnostic material or radiotherapeutic materials; and
• non-hazardous or general waste: waste that does not pose any particular biological,
chemical, radioactive, or physical hazard.

The major sources of healthcare waste are:

• hospitals and other health facilities • animal research and testing
• laboratories and research centres laboratories
• mortuary and autopsy centres • blood banks and collection services
• hospital wards • nursing homes for the elderly

Management of healthcare waste

Hospital waste is a potential reservoir of pathogenic micro-organisms and requires appropriate,
safe, and reliable handling. The main risk associated with infection is sharps contaminated with
blood. There should be a person or persons responsible for the organization and management of
waste collection, handling, storage, and disposal. Waste management should be conducted in
coordination with the infection control team.
Steps in the management of hospital waste include:
- generation, - storage,
- segregation/separation, - treatment,
- collection, - Final disposal.
- transportation,
Waste management practices must meet national and local requirements; the following principles
are recommended as a general guide:

40
Principles of waste management
- Develop a waste management plan that is based on an assessment of the current
situation, and which minimizes the amount of waste generated.
- Segregate clinical (infectious) waste from non-clinical waste in dedicated containers.
- Transport waste in a dedicated trolley.
- Store waste in specified areas with restricted access.
- Collect and store sharps in sharps containers. Sharps containers should be made of
plastic or metal and have a lid that can be closed. They should be marked with the
appropriate label or logo, e.g. a biohazard symbol for clinical (infectious) waste Mark
the storage areas with a biohazard symbol.
- Ensure that the carts or trolleys used for the transport of segregated waste collection
are not used for any other purpose - they should be cleaned regularly.
- Identify a storage area for waste before treatment or being taken to the final disposal
area.

Additional (transmission-based) precautions

Additional (transmission-based) precautions are taken while ensuring standard precautions are
maintained. Additional precautions include:
- Airborne / Droplet precautions.
- Contact precautions.

41
Airborne /Droplet precautions
- The following precautions need to be taken:
- Implement standard precautions.
- Place the patient in a single room that has a monitored negative airflow pressure and is
often referred to as a “negative pressure room”. The air should be discharged to the
outdoors or specially filtered before it is circulated to other areas of the health care
facility.
- Keep doors closed.
- Anyone who enters the room must wear a special, high filtration, particulate respirator
(e.g. N 95) mask.
- Limit the movement and transport of the patient from the room for essential purposes
- only. If transport is necessary, minimize the dispersal of droplet nuclei by masking the
patient with a surgical mask.

Contact precautions
- Diseases that are transmitted by this route include colonization or infection with multiple
antibiotic-resistant organisms, enteric infections, and skin infections.
- The following precautions need to be taken:
- Implement standard precautions.
- Place the patient in a single room (or in a room with another patient infected by the same
pathogen). Consider the epidemiology of the disease and the patient population when
determining patient placement.
- Wear clean, non-sterile gloves when entering the room.
- Wear a clean, non-sterile gown when entering the room if substantial contact with the
patient, environmental surfaces, or items in the patient’s room is anticipated.
- Limit the movement and transport of the patient from the room; patients should be moved
for essential purposes only. If transportation is required, use precautions to minimize the
risk of transmission.

Cleaning, Disinfection and Sterilization

Cleaning
Before any reprocessing to achieve disinfection or sterility, all instruments and equipment MUST
be cleaned. If not cleaned properly, organic matter may prevent the disinfectant or sterilant from
having contact with the instrument/equipment and may also bind and inactivate the chemical
activity of the disinfectant. If an instrument/equipment is unable to be cleaned, then it is unable to
be sterilized or disinfected.

After an instrument has been used, prior to drying, it should be washed to remove any gross soiling.
At this stage, detergent and water are appropriate to use.
There are four main methods used for cleaning of instruments and equipment:

42
 1. Manual cleaning
2. Enzymatic cleaners
3. Ultrasonic cleaners and automated washers
4. Disinfection

Disinfection
- Disinfection removes microorganisms without complete sterilization.
- Disinfection is used to destroy organisms present on delicate or heat-sensitive instruments
which cannot be sterilized or when single use items are not available.
- Disinfection is not a sterilizing process and must not be used as a convenient substitute for
sterilization. Thermal disinfection is not appropriate for instruments that will be used in
critical sites as these instruments must be sterile.
- Certain products and processes will provide different levels of disinfection.
These levels are classified as:
• High-level disinfection: Destroys all microorganisms except some bacterial spores
(especially if there is heavy contamination).
• Intermediate disinfection: Inactivates Mycobacterium tuberculosis vegetative bacteria,
most viruses, and most fungi, but does not always kill bacterial spores.
• Low-level disinfection: Can kill most bacteria, some viruses, and some fungi, but cannot
be relied on to kill more resistant bacteria such as M. tuberculosis or bacterial spores.

The two methods of achieving disinfection are thermal and chemical disinfection.
Thermal disinfection (pasteurization)
- If an instrument is able to withstand the process of heat and moisture and is not required
to be sterile, then thermal disinfection is appropriate.
- Using heat and water at temperatures that destroy pathogenic, vegetative agents, is a very
efficient method of disinfection.
- The level of disinfection depends on the water temperature and the duration the instrument
is exposed to that temperature.

Chemical disinfection
- The performance of chemical disinfectants is dependent on a number of factors including
temperature, contact time, concentration, and pH, the presence of organic or inorganic
matter, and the numbers and resistance of the initial bio-burden on a surface
- Instrument grade disinfectants are classified as high, intermediate, or low level. When used
according to the manufacturers’ guidelines, disinfectants will fall into one of these levels.

Sterilization
Sterilization is defined as the process where all living microorganisms, including bacterial spores,
are killed. Sterilization can be achieved by physical, chemical, and physiochemical means.

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Sterilization is the destruction of all microorganisms and can be achieved by either physical or
chemical methods.

Sterilization is necessary for medical devices penetrating sterile body sites. Cleaning to remove
visible soiling in reusable equipment should always precede sterilization. All materials must be
wrapped before sterilization. Only wrapped/packed sterilized materials should be described as
sterile. Before any instrument or equipment goes under the process of steam sterilization, the
following should be checked:
- Ensure that the instrument can withstand the process (e.g. steam under pressure),
- Ensure that the instrument has been adequately cleaned,
- Ensure that the instrument does not require any special treatment,
- Ensure that records of the sterilization process and the traceability of instruments are kept.
Instruments and equipment will only be sterile if one of the following sterilizing processes is used:
1. Steam under pressure (moist heat),
2. Dry heat,
3. Ethylene oxide,
4. Automated environmentally sealed low-temperature peracetic acid, hydrogen peroxide
plasma and other chemical sterilant systems or sterilants, or
5. Irradiation.

1. Steam under pressure (moist heat) sterilization

This is the most efficient and reliable method to achieve sterility of instruments and
equipment. This method sterilizes and dries the sterile package as part of the cycle.
2. Dry heat sterilization (hot air ovens)

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 Dry heat sterilization is caused by hot air that destroys pathogens by the process of
oxidation. Dry heat sterilizers have had limited value because it is difficult to
maintain the same temperature throughout the load, while the high temperatures
and long time (170 o C for 1 hour) required to achieve sterility make this method
undesirable for many situations.
3. Ethylene Oxide (EO)
Ethylene oxide gas is appropriate to use for the sterilization of instruments/
equipment made from heat-labile materials or devices that contain electronic
components. The time required to process the instrument is dependent on the
temperature, humidity, and concentration level of the gas.

The gas must penetrate the packaging and reach all surfaces of the
instrument/equipment requiring sterilization. The time for such a process is
between 12 hours to over 24 hours. Because EO is toxic, this gas is restricted in
healthcare facilities and must be used according to strict guidelines to ensure staff
safety
4. Automated chemical (low temperature) systems
Hydrogen peroxide plasma in a fully automated cycle can achieve low temperature,
and low moisture sterilization within a 45–80-minute cycle depending on the model
of sterilizer used.
5. Irradiation
Gamma radiation is available from some commercial gamma irradiation facilities.
However, it is not readily available for use in healthcare facilities. Only those
instruments and equipment that have undergone the entire sterilizing process can
be regarded as sterile. Items must be wrapped or packaged appropriately to be
considered sterile

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SIMPLE LABORATORY TESTS
SPECIMEN COLLECTION
Collection of material for bacteriological examination is the responsibility of the nurse. The
specimen should be collected in such a manner that it does not become contaminated with other
organisms.
▪ Preferably specimens should be obtained before antibiotics or other antimicrobial agents
are administered. If culture has been taken after initiation of antimicrobial therapy,
the laboratory should be informed so that specific counteractive measures such as adding
penicillinase or merely diluting the sample may be carried out.
▪ Material should be collected from a region where the suspected organism is most likely to
be found and with as little external contamination as possible.
▪ Another important point to remember is the stage of the disease. Enteric pathogens are
present in much larger numbers during another acute diarrheal stage of intestinal infections
and they are most likely to be isolated at that time.
▪ Specimen should be quantitatively sufficient to permit complete examination and should
be kept in sterile containers. Arrangements should be made for prompt delivery of
specimens to the laboratory.
▪ The laboratory should be provided with sufficient clinical information to guide the
microbiologist in the selection of suitable media and appropriate techniques.

Important points to remember are:

1. Strict aseptic precautions
2. Use always sterile containers labeled with the patient’s hospital number.
3. Avoid soaking outside of containers
4. Proper transport. If a delay is expected, refrigerate the specimens

SAMPLES USED
1. URINE
Midstream or clean-catch specimen is to be obtained. The specimen must be collected in a sterile,
wide mouthed screw capped bottle, after thoroughly cleaning the genitalia with soap and water.
Improperly collected urine specimens will lead to incorrect lab reports. The specimen must reach
the laboratory within 15 minutes of collection. If not, it should be refrigerated immediately. If
infection with tuberculosis is suspected, the entire early morning sample of urine should be sent in
a large special sterile bottle.
2. FEACES
A small quantity of formed stool is placed in a sterile specimen container. About one third of the
container should be filled with the stool. The container should never be completely filled with
stool. Special care should be taken to see that the outside of the container is not contaminated. If
mucus or flakes of tissue is present in the feces, these should be included in the collected specimen.
In certain cases, like suspected bacillary dysentery or Escherichia coli diarrhea, rectal swab is

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preferred. Sterile swabs, moistened in sterile saline are introduced well beyond the internal
sphincter, twirled well, gently withdrawn and placed in a sterile test tube, and sent to the laboratory
immediately.
3. PUS OTHER THAN PURULENT BODY FLUID
About 1mL of pus is placed in a sterile test tube. If this is not possible as much pus as possible is
collected on two sterile swabs and replaced in a sterile test tube. The end of the swab sticks is
never to be broken off. The tips of the swab sticks should project beyond the mouth of the tube to
facilitate handling. The mouth of the test tube with projected tips of the swab sticks must be secured
with sterile cotton or gauze fastened with adhesive tapes soon after collection.
Sputum
As far as possible, an early morning coughed up specimen is preferred. Instruct the patient to wash
the mouth with plain water, a few minutes before taking the specimen. A few milliliters of the
coughed-up specimen are placed in a sterile wide mouthed, screw-capped bottle and dispatched as
early as possible.
4. BLOOD
Blood for serological Tests
For investigation 10mL of blood should be taken in a dry syringe and placed in a sterile test tube
or bottle. The bottle should not contain any anticoagulant. The blood should be allowed to clot.
The blood should be placed in the container directly from the syringe after removing the needle to
avoid hemolysis due to frothing (forcing blood through the needle can cause hemolysis).
Blood for cultures
Cultures are made to determine the presence or absence of bacteria and therefore should be taken
by venipuncture under careful aseptic conditions. The blood is added to the culture media in glass
tubes and cultivated. It is observed after a period of time usually 2 to 3 days. Some of the organisms
that can be determined by means of blood cultures are typhoid bacilli, pneumococci, streptococci
and staphylococci.
Blood for Widal test
Widal test is a specific test for antibodies produced by typhoid and paratyphoid bacilli within the
blood and tissues. Blood is collected by a sterile syringe and needle. The serum is allowed to
separate from the clot. When various dilutions of the serum are made with normal saline and a
standard antigen prepared with killed organism is mixed with the serum, agglutination will take
place in a positive test.

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