Ch1: INTRODUCTION

1) Microbiology is the science that deals with the study of microorganisms.

2) Microorganisms are organisms that require microscope to be observed.
3) Microbiology plays a role in:
a. Disease control
b. Development of pharmaceutical products
c. Quality control method
d. Biotechnology
Microorganisms are used to produce vitamins, amino acids, enzymes & growth
4) There are different types of microbes: bacteria fungi algae protozoa viruses
5) Microorganisms are classified based on cell type into eukaryotes and prokaryotes.
Eukaryote is an organism that possesses a clearly defined nucleus; e.g. fungi, protozoa
Prokaryote is an organism characterized by the absence of a distinct membrane bound
nucleus or membrane bound organelles; e.g: bacteria

6)

7) Bacteria: classified as prokaryotes, which are single‐celled organisms with a

simple internal structure that lacks a nucleus
Bacteria can live in soil, water and inside the human body.
Bacteria can be classified into: normal flora, pathogen and opportunistic
pathogen. Reproduce by budding
8) Viruses
Viruses do not have a cellular structure. A virus consists of DNA or RNA molecule surrounded by a
protein coat.
A complete virus particle or virion is made up of:
A. core of genetic material either DNA or RNA
B. protective coat called capsid made up of protein
C. Sometimes the capsid is surrounded by an additional layer a lipid
1) membrane envelope
9) Fungi eukaryotic group May be unicellular or multicellular Non motile
Reproduce by budding
10) Protozoa are single celled, eukaryotic organisms.
Many protozoa are free living, but others are among the most clinically
important parasites of humans.
Ch2: Introduction to Bacteria
1) Different shapes of bacteria Cocci Chain = Streptococcus Cluster = Staphylococcus
Bacilli Chain = Streptobacillus Coccobacillus Vibrio = curved Spirillum Spirochete Square Star
2) Bacterial Cell Structures: Flagella/ Pili/Capsule/ Plasma Membrane/ Cytoplasm/ Cell Wall/
Lipopolysaccharides/ Teichoic Acids/Inclusions/ Spores
3) Bacterial reproduction
Generation time: The time cell takes to divide (double)
Bacterial reproduction: Binary Fission
Division exactly in half
Most common means of bacterial reproduction
Forming two equal size progenies
Genetically identical offspring
Cells divide in a geometric progression doubling cell number
4) Classification of bacteria
Bacteria are classified into gram positive and gram negative according to cell wall structure.
Gram positive bacteria
5) Cell walls of gram‐positive bacteria are very thick and consist primarily of
peptidoglycan.
 Most gram‐positive cell walls contain additional substances such as teichoic acid.
 The periplasmic space of gram‐ positive bacteria lies between plasma membrane and cell
wall.
6) Gram negative bacteria
 Cell walls of gram‐ negative bacteria consist of two layers; a thin peptidoglycan layer
and a thick outer membrane containing lipopolysaccharide molecules (LPS).
 It is much more complex than gram positive wall
 The periplasmic space of gram‐negative bacteria lies between the outer ‐membrane and
the cell wall.
 Outer membrane
 The outer membrane is unique to gram‐negative negative bacteria and lies outside the
peptidoglycan layer.
 The membrane consists of a phospholipid bilayer in which a large proportion of these phospholipid
molecules are replaced by lipopolysaccharide molecules (LPS).
 lipopolysaccharide (LPS) of the outer membrane is also called endotoxin.
lipopolysaccharide (LPS) consists of three parts:
1. lipid A
2. core polysaccharide
3. O‐somatic antigen
Function of lipopolysaccharide (LPS)
 bacterial attachment to surfaces & biofilm formation.
 creating a barrier restricting the entry of toxic substances that might kill or
injure the bacterium.
 protecting pathogenic gram‐negative bacteria from host defense.
 The O side chain elicits an immune response and is responsible of production of
antibodies.
 The lipid A domain is responsible for much of the toxicity of Gram‐negative bacteria.
When bacterial cells are lysed by the immune system, fragments of membrane
containing lipid A are released into the circulation, causing fever, diarrhea, and possible
septic shock.
Ch 3: Microbial pathogenicity
 Pathogen is a microorganism that is able to cause disease in a plant, animal or human.
 Pathogenicity is the ability to produce disease in a host organism.
 Virulence is the degree of causing disease of the microbe.
Mechanism of bacterial pathogenesis
 Pathogenicity in bacteria may be associated with unique structural components
of the cells or active secretion of substances.
 In order to cause disease, pathogens must:
1. Gain access to the host (through portal of entry)
2. Adhere to host tissues
3. Penetrate host cell and escape/ evade host defenses
4. Damage host tissue (either directly by accumulation of waste products or
by production of toxins).
1‐ Portal of entry
Mucous membrane(respiratory tract) /skin & parenteral route
2‐Adherence
• Adherence is the ability of pathogen to attach to host tissues at portal of entry.
• Bacteria usually employ proteins known as adhesin for the attachment process.
• Attachment also occurs through ligands present on pathogen that bind to receptor on
host cell (sugar).
• Most microbial adhesins are glycoproteins or lipoproteins located on the glycocalyx,
capsule, capsid, pili, fimbriae or flagella.
3‐Escaping host defenses
Most successful pathogens, possess additional structure or biochemical features which allow
them to resist host defense such as: damage to host
 Capsules that protect against phagocytosis
 Enzymes: many pathogens secrete enzymes that contribute to their
pathogenicity.
 Antigenic variation: Some microbes can change surface antigen to escape the
attack by antibodies ex: influenza Virus
4‐ Damage to host tissues
Bacteria have the ability to cause damage by:
 Using host’s nutrients:
Iron is required for growth of most pathogenic bacteria. In humans, iron is bound to iron ‐transport
protein. To obtain free iron, pathogen secrete siderophore proteins that bind iron more strongly than
transport proteins.
 Direct damage: Pathogen cause direct damage to cells by using host nutrients and producing waste
products or by multiplying inside cells causing cell rupture.
 Production of toxins: There are two types of toxins produced by
bacteria: exotoxin and endotoxin
Exotoxin: Exotoxins are soluble proteins secreted by living bacteria during exponential growth
 The production of this type of toxins is generally specific to a particular bacterial species. Virulent
strains of the bacterium produce the toxin (or range of toxins) while nonvirulent
strains do not.Both Gram‐positive & Gram‐negative bacteria produce exotoxins
 Endotoxin are part of the outer cell wall of bacteria
These toxins are associated with Gram negative bacteria as constituents of the outer membrane of the cell
wall. The biological activity of endotoxin is associated with the lipopolysaccharide (LPS)
Chap 4: Normal flora
Normal microbial flora is a population of microorganisms that are present in the skin and mucous
membranes of healthy normal persons.
Microbial flora differs by: individual/ age/ geographic location/ health status/ diet
Host‐microbe relationships can be:
 Positive (mutualistic)
 Neutral (commensalistic)
 Negative (parasitic or pathogenic)
Mutualistic: a relationship between two species of organisms in which both benefit from the association
Commensalistic: A relationship between two organisms of different species in which one
derives some benefit while the other is unaffected
Parasitic: relationship in which the microbe benefits at the expense of the host. microbe causes damage
to the host.
Role of NORMAL FLORA: In most cases, Host‐microbe relationship will remain positive :
 host provides a nutrition for the colonizing microbes
 microbe occupies a space that a potential parasite orpathogen might colonize.
 microbial communities may even aid in digestion or synthesize nutrients for the host.
Location of normal flora
Normal flora can be found in many sites of the human body including:
 skin (staphylococcus aureus)
 respiratory tract
 urinary tract
 digestive tract
Areas of the body such as brain, circulatory system &lungs are intended to remain sterile (microbe
free)
Chap 5: Nosocomial Infections:
Nosocomial infection is defined as an infection acquired in hospital by a patient in
whom the infection was not present or incubating at the time of admission.
The most common types of Health care associated infections (HAIs) are:
 urinary tract infections
 surgical site infections
 Gastroenteritis
 Meningitis
 Pneumonia
 blood stream infection
Symptoms for these infections may include:
 discharge from a wound
 fever
 cough, shortness of breathing
 burning with urination or difficulty urinating
Bacteria, fungus, and viruses can cause nosocomial infections
Bacteria alone cause about 90 percent of these cases
Nosocomial infections result from the interaction of several factors:
 The microbial agent
 Patient susceptibility
 Environmental factors
The microbial agent:
The most common pathogens that cause nosocomial infections are:
 Staphylococcus aureus
 Pseudomonas aeruginosa
  Esherichia coli
 Acinetobacter baumanii
The source of infection can be endogenous (normal flora) or exogenous (outer source)
Preventing nosocomial infections
General preventive measures
1‐Observing hand hygiene
Hands are the most common vehicle for transmission of organisms.
Hand hygiene is the single most effective mean of preventing the horizontal transmission of infections
among hospital patients and health care personnel.
According to the World Health Organization (WHO), there are Five Moments for Hand Hygiene:
1. Before Patient Contact.
2. Before and Antiseptic Task.
3. After Body Fluid Exposure Risk.
4. After Patient Contact.
5. After Contact with Patient Surroundings.
2‐ Monitoring the use of antibiotics in the hospital.
3‐ Regular change of surface antibacterial for the bacteria do not become resistant products
4‐ Constitution of a committee for the fight against nosocomial infections
5‐ Reducing the length of stay of the patient is an effective method of reducing the rate of nosocomial
infections
Chap 6: vaccination:
A vaccination is the injection of a killed or weakened organism that produces immunity
in the body against that organism.
Bacterial vaccine types
• Live attenuated bacterial vaccines
• Killed bacterial vaccines
• Toxoid vaccines
• Capsular polysaccharide and polypeptide vaccines
• Purified protein vaccines
1) Live attenuated vaccines
Virulent pathogenic organisms are treated to become attenuated and avirulent but antigenic.
Examples:
 Vaccination against Tuberculosis disease:
 Vaccination against Typhoid fever: Contains live, attenuated Salmonella typhi. It is indicated
for persons living or traveling in areas where there is a high risk of typhoid fever and for
persons in close contact with either infected patients or chronic carriers.
2) Toxoid vaccine
They are prepared by detoxifying the exotoxins of some bacteria
Examples:
 Corynebacterium diphtheriae vaccine
 Clostridium tetani vaccine This vaccine contains tetanus toxoid. It is given to everyone both
early in life and later as boosters for protection against tetanus.
3) Killed bacterial vaccine
Example:
Vibrio cholerae vaccine
Chap 7: food‐borne diseases
Foodborne illness is caused by consuming contaminated foods or beverages. Most foodborne diseases are
infections caused by a variety of bacteria, viruses, and parasites.
Foodborne diseases are classified into:
1‐ Food‐borne infections Food borne infection is caused by ingestion of food containing live bacteria
which grow and establish themselves in human intestinal tract.
2‐ Food‐born intoxications Food borne intoxications is caused by ingesting food containing toxins formed
by bacteria which resulted from the bacterial growth in food item.
The symptoms of food poisoning range from mild stomach cramps to nausea, vomiting,
diarrhea, and fever, which can be life‐threatening to very young children, pregnant women, and
people whose immune systems are already weakened.
Bacterial causes of diarrhea
1) Cholera: Cholera is an acute diarrheal disease caused by gram negative vibrio cholera bacterium.
 Mode of transmission
The main mode of transmission is through contaminated water and food, or person ‐to ‐person
spread in overcrowded, unhygienic situations.
 Clinical features:
After an incubation period of 24 – 48 hours, patients experience sudden watery diarrhea
accompanied by vomiting. Fever and abdominal pain are usually absent. Important
complications include dehydration, shock, electrolyte disturbances and acute renal failure.
 Treatment: Oral rehydration Tetracyclines
2) Brucellosis
Brucella species are small Gram‐negative coccobacilli, which are part of the normal flora of the
genitourinary tract of cows, goats, sheep, pigs, and dogs.
 Mode of transmission:
1‐Ingestion of unpasteurized raw dairy products
2‐Direct contact with infected animals.
 Clinical Features
The incubation period for Brucella infections ranges from five days to several months.
Symptoms are nonspecific and flulike. Untreated, patients may develop an undulating pattern of
fever (temperatures repeatedly rise then fall, hence the name “undulant fever” is the traditional
name for brucellosis). Manifestations of brucellosis may involve any of a variety of organ
systems, including the GI tract, and the skeletal, neurologic, cardiovascular, and pulmonary
systems.
 Treatment:
Combination therapy. Prolonged treatment (for example, six weeks) is generally
necessary to prevent relapse and to reduce the incidence of complications
3) Salmonella
Members of the genus Salmonella can cause a variety of diseases, including gastroenteritis and
enteric (typhoid) fever.
 Mode of transmission:
Salmonella invades epithelial cells of the small intestine. Disease may remain localized or
become systemic.
 Clinical features:
o Gastroenteritis: This localized disease is caused primarily by (nontyphoidal
salmonella). It is characterized by nausea, vomiting, and diarrhea (usually nonblood),
which develop generally within 48 hour sof ingesting contaminated food or water.
Fever and abdominal cramping are common.
o Enteric (typhoid) fever: This is a severe, life-threatening systemic illness,
characterized by fever and, frequently, abdominal symptoms. It is caused primarily
by serotype typhi (typhoidal salmonella). Nonspecific symptoms may include chills,
sweats, headache, anorexia, weakness, sore throat, cough, myalgia, and either
diarrhea or constipation. The incubation period varies from 5 to 21 days.
  Treatment:
For gastroenteritis in uncompromised hosts, antibiotic therapy is often not needed, and may
prolong the convalescent carrier state. For enteric fever, appropriate antibiotics include β‐
lactams and fluoroquinolones. Prevention of salmonella infection is accomplished by proper
sewage disposal, correct handling of food, and good personal hygiene.
4) Escherichia coli
E. coli is part of the normal flora in the colon of humans and other animals. Diseases caused by E.
coli can be gastrointestinal and/or extraintestinal. There are different strains of Escherichia coli which
give rise to diarrhea by different mechanisms.

Viral food‐borne diseases

1) Hepatitis A
Hepatitis A virus (HAV) is a member of the genus hepato ‐virus.
 Mode of Transmission
Transmission is by the fecal‐oral route, and the virus is shed in the feces.
 Symptoms: Fatigue/Sudden nausea and vomiting/Abdominal pain or discomfort, especially on the
upper right side/ Clay‐colored bowel movements/ Low‐grade fever/ Yellowing of the skin and the
whites of your eyes (jaundice)/ Intense itching
 Treatment: Immune globulin is used as postexposure prophylaxis. No antiviral agents are
currently available for treating HAV infections.
 Prevention: Vaccines prepared from whole virus inactivated are now available. Immune globulin
has been used for many years, mainly as postexposure prophylaxis. Prevention of HAV infection
requires taking measures to avoid fecal contamination of food and water.
Parasitic food‐borne diseases
1) Toxoplasmosis: Toxoplasmosis is caused by an intracellular parasite known as
Toxoplasma gondii.
 Mode of Transmission
Transmission is by accidental ingestion of cat feces, eating raw or undercooked meat,
from an infected mother to fetus, or from a blood transfusion.
 Symptoms swollen lymph glands, especially around the neck. Muscle aches and
pains. Headache. Fever. Generally feeling unwell. Inflammation of the lungs.
Inflammation of the heart muscle. Inflammation of the eye
  Treatment
The treatment of choice for this infection is the antifolate drug pyrimethamine, given
in combination with sulfadiazine.
2) Taeniasis
This form of the disease is caused by the larval form of Taenia saginata (beef
tapeworm). The disease is transmitted by larvae in undercooked or raw beef.
 Symptoms most no symptoms or mild symptoms. Tapeworms can cause digestive
problems including abdominal pain, loss of appetite, weight loss, and upset stomach.
The most visible symptom of taeniasis is the active passing of proglottids (tapeworm
segments) through the anus and in the feces.
 Treatment Taeniasis is typically treated with praziquantel and albendazole.
Chap 8: Blood‐borne infections
Bloodborne disease, any of a group of diseases caused by pathogens such as viruses or bacteria that are
carried in and spread through contact with blood. Common bloodborne diseases include hepatitis B,
hepatitis C, and human immunodeficiency virus (HIV).
1) Hepatitis B and C
Hepatitis is an inflammation of the liver. The condition can be self‐limiting or can progress to fibrosis
(scarring), cirrhosis or liver cancer. Hepatitis viruses are the most common cause of hepatitis in the world.
Symptoms of hepatitis can include: fever, fatigue, loss of appetite, nausea, vomiting, abdominal pain,
dark urine, light‐colored stools, joint pain, and jaundice.

2) HIV Human immunodeficiency virus (HIV)

is a non‐oncogenic retrovirus. Transmission occurs
mainly by one of three routes: sexually with blood or blood products, perinatally (from mom to fetus)
Several weeks after the initial infection, during which there is a very high level of virus replication in
CD4+ cells. Lymph nodes become infected, which are the sites of virus persistence during the
asymptomatic period.
The acute phase viremia resolves into a clinically asymptomatic or "latent" period lasting from months to
many years. This period is characterized by persistent generalized lymphadenopathy diarrhea, and weight
loss.
Chap 9: Diseases transmitted by skin contact
1) Rabies
Humans are usually infected by the bite of an animal. Following inoculation, the virus may replicate
locally, but then travels via the axoplasm of peripheral neurons to the brain, where it replicates
primarily in the gray matter.
 Symptoms
Clinical illness may begin with an abnormal sensation at the site of the bite, then progress to a
fatal encephalitis, with neuronal degeneration of the brain and spinal cord.
Symptoms include hallucinations, seizures, weakness, mental dysfunction, paralysis, coma, and
finally death. Many, but not all, patients show the classic rabid sign of hydrophobia.
2) Herpes
The herpes simplex virus is a contagious virus that can be transmitted from person to person
through direct contact. They then carry the virus with them for the rest of their lives.
 Symptoms
Flu‐like symptoms such as swollen lymph nodes and headache.
redness, swelling, pain, or itching where the infection will erupt painful, fluid‐filled blisters on
the lips or under the nose. cold sores of fever blisters on or around the mouth.
 Treatment Acyclovir
3) Mumps
Mumps is a contagious disease caused by mumps virus
 Mode of transmission
It spreads through direct contact with saliva or respiratory droplets from the mouth, nose, or throat.
 Symptoms Mumps is best known for the puffy cheeks and tender, swollen jaw that it causes. This
is a result of swollen salivary glands under the ears on one or both sides, often referred to as
parotitis.
 Treatment is symptomatic.
4) Warts
Warts are a type of skin infection caused by the human papillomavirus (HPV). The infection
causes rough, skin‐colored bumps to form on the skin.
 Mode of transmission The virus can spread from person to person or from different parts of
the body through: Direct contact with a wart. Touching something contaminated with the
virus, such as towels, doorknobs and shower floors.
 Treatment Stronger peeling medicine (salicylic acid).
2. Freezing (cryotherapy)
3. Minor surgery
4. Laser treatment
5) Scabies
Scabies is an itchy skin condition caused by a tiny burrowing mite called Sarcoptes scabiei.
Scabies is contagious and can spread quickly through close physical contact in a family, child
care group, school class and nursing home. Intense itching occurs in the area where the mite
burrows. The urge to scratch may be especially strong at night.
Treatment
Permethrin cream
Ivermectin
Crotamiton lotion
6) Tetanus
Tetanus is an infection caused by a bacterium called Clostridium tetani. Spores of tetanus
bacteria are everywhere in the environment, including soil, dust, and manure. The spores
develop into bacteria when they enter the body.
  Mode of transmission
The spores can get into the body through broken skin, usually through injuries from
contaminated objects. Tetanus bacteria are more likely to infect certain breaks in the skin.
 Symptoms Jaw cramping Sudden, involuntary muscle tightening (muscle spasms) Painful
muscle stiffness all over the body Trouble swallowing seizures
 Treatment Tetanus is a medical emergency requiring:
Care in the hospital
Immediate treatment with medicine called human tetanus immune globulin (TIG)
Drugs to control muscle spasms
Antibiotics
Tetanus vaccination
Chap 10: Airborne diseases
Airborne diseases are caused by pathogenic microbes small enough to be discharged from an
infected person via coughing, sneezing, laughing and close personal contact or aerosolization
of the microbe.
1) Chicken pox
Chickenpox is an infection caused by the varicella‐zoster virus.
 Mode of transmission
Varicella is highly contagious. The virus can be spread from person to person by direct contact,
inhalation of aerosols from vesicular fluid of skin lesions of acute varicella or zoster, and
possibly through infected respiratory secretions that also may be aerosolized.
 Symptoms
The classic symptom of chickenpox is a rash that turns into itchy, fluid‐filled blisters. The rash
may first show up on the chest, back, and face, and then spread over the entire body, including
inside the mouth, eyelids, or genital area. It usually takes about one week for all of the blisters
to become scabs.
 Treatment: acyclovir anti‐histamine
2) Measles
Measles is a highly contagious infectious disease caused by measles virus. Symptoms
usually develop 10–12 days after exposure to an infected person.
 Mode of transmission
Measles is a highly contagious virus that lives in the nose and throat mucus of an infected
person. It can spread to others through coughing and sneezing.
 Symptoms: high fever rash cough runny nose red watery eyes
Tiny white spots (Koplik spots) may appear inside the mouth two to three days
after symptoms begin
There's no specific treatment for measles.
3) Viral rhinitis
Rhinitis is a group of disorders characterized by inflammation and irritation of mucus
membrane of the nose.
Common causes of viral rhinitis include rhinovirus, coronavirus, adenovirus, influenza
virus, parainfluenza virus, respiratory syncytial virus, and enterovirus
 symptoms
runny nose, sneezing, congestion, postnasal drip, cough, and a low‐grade fever.
Treatment is supportive Decongestant Bed rest Analgesics
4) Influenza
Influenza is an acute viral infection of the upper or lower respiratory tract caused by by
Influenza viruses are categorized as types A, B, C, and D.
 Mode of transmission: infection is transmitted from person to person through the respiratory
tract, by such means as inhalation of infected droplets resulting from coughing and sneezing.
  Symptoms Fever Dry, persistent cough Shortness of breath Tiredness and weakness Runny or
stuffy nose Sore throat Eye pain
 Treatment Rest Anti‐pyretic (for fever) Analgesic (for pain) Antiviral agents: oseltamivir
(Tamiflu)
5) Pertussis
Pertussis, also known as whooping cough, is a highly contagious respiratory disease. It is caused by
the bacterium Bordetella pertussis.
 Treatment
The recommended antimicrobial agents for treatment or chemoprophylaxis of pertussis are
Azithromycin Clarithromycin
6) Diphtheria
Diphtheria is a serious infection caused by strains of bacteria called Corynebacterium
diphtheriae that make toxin (poison).
 Mode of transmission
Diphtheria bacteria spread from person to person, usually through respiratory droplets, like
from coughing or sneezing.
 Symptoms
a thick grey‐white coating at the back of your throat.
a high temperature (fever) of 38C or above swollen glands in your neck.
 Treatment Antibiotics