Sem IV (2023-24)

• I will be teaching
• SBT403 Unit 1 Overview of medical microbiology
• SBT403 Unit 2 Infectious agents I
• SBT407 Unit 1 Entrepreneurship
Medical microbiology
SBT 403
Unit 1
Overview of medical
microbiology
Subunits
•Normal microbiota of human body
•Principles of Diseases
•Mode of transmission of infection
•Pathogenicity
•Diagnosis
•Prophylaxis
•Epidemiology
 Healthy
Defenses human
being

We are still susceptible to

pathogens!!!

Pathogen is a disease causing microorganism

 •Defenses
•Pathogenic mechanism of microorganisms

A delicate balance exists between our defenses and the pathogenic

mechanisms of microorganisms
 •Defenses
•Pathogenic mechanism of
microorganisms

When our defenses resist these pathogenic capabilities, we

maintain our health
 •Pathogenic mechanism of microorganisms
•Defenses

When the pathogen’s capabilities overcome our

defenses, disease results!!!
 Disease has become established

Suffer
Temporary
Completely
recover
Permanent
Damage
Die
Question-
• Are all microbes pathogens???
• Are non pathogenic microbes present around us or on us, are good
for us?
 Normal microbiota of human body
• Definition - Microorganisms harbored in or on human body that are
more or less constant are called the normal microbiota or normal
flora of human body
• Types – Resident and Transient
• Resident - A constant microbial population that cannot be
completely removed permanently
• Transient – A microbial population that varies time to time and is
temporary
• Normal flora may be saprophytes, commensals,
opportunistic/facultative pathogens and true pathogens
Significance of normal microflora of human
body
A normal micro flora plays an important role in economy of human
body-
1. They can become pathogenic when host immune system falter
2. They can prevent or interfere with colonization/ invasion of body by
pathogens
3. They raise the overall immune status of the host against the
pathogen having some related or shared antigens
4. They cause confusion in diagnosis due to their ubiquitous presence
in the body and their resemblance with the pathogen
5. They may produce disease if introduced into foreign locations in
large numbers.
Some specific examples
1. Microflora of intestinal tract synthesise vitamin K and vitamin B
2. Some microorganisms produce the antibiotic substance ‘colicins’
which is harmful to pathogens
3. Some microbes produce endotoxins. These endotoxins trigger
alternative complement pathway (Safe as long as not produced in
excess amounts)
4. Opportunistic pathogen can multiply and cause enteritis and
endotoxic shock
5. Penicillinase producing organism can aggravate infection by
interfering with the therapy
6. Certain Streptococci of mouth cause dental carries
Origin of normal flora- source of microflora on a new
born
We are going to study-
1. Source of microflora on a new born
2. Difference in microflora of-Vaginally delivered infants and Infants
delivered via C-section
3. Normal flora-on skin, teeth and upper respiratory tract, intestine
and vagina of a new-born
Origin of normal flora- source of microflora on a new
born

• At its earliest stage of community development (<5 minutes

postdelivery), the human microbiota is homogeneously distributed
across the body.
 Origin of normal flora-Difference in microflora
of-Vaginally delivered infants
and Infants delivered via C-section
Vaginally delivered infants Infants delivered via C-section
Harbor bacterial communities (in all body Harbor bacterial communities (across all
habitats) that are most similar in body habitats) that are most similar to the
composition to the vaginal communities of skin communities of the mothers
the mothers
Lactobacillus, Prevotella, Atopobium, and Staphylococcus, Corynebacterium, or
Sneathia spp. Propionibacterium spp.
Remember the examples No spelling mistakes
Origin of normal flora-on teeth and upper respiratory
tract
• Within 4–12 hours after birth, viridans streptococci become established as
the most prominent members of the resident flora and remain so for life.
Alpha haemolytic streptococci appear in upper respiratory tract.
• Early in life, aerobic and anaerobic staphylococci, gram-negative diplococci
(Neisseriae, Moraxella catarrhalis), diphtheroids, and occasional lactobacilli
are added
• When teeth begin to erupt, the anaerobic spirochetes, Prevotella species
(especially Prevotella melaninogenica), Fusobacterium species, Rothia
species, and Capnocytophaga species establish themselves along with
some anaerobic vibrios and lactobacilli
• Small bronchi and alveoli are normally sterile
 Origin of normal flora-in intestine

• At birth, the intestine is sterile, but organisms are soon introduced

with food.
 Origin of normal flora-in vagina
• Soon after birth, aerobic lactobacilli (Doderlien’s bacilli) appear in the
vagina and persist as long as the pH remains acidic (several weeks). When
the pH becomes neutral (remaining so until puberty), a mixed flora of cocci
and bacilli is present.

• At puberty, aerobic and anaerobic lactobacilli reappear in large numbers

and contribute to the maintenance of acid pH through the production of
acid from carbohydrates, particularly glycogen.

• This appears to be an important mechanism in preventing the

establishment of other, possibly harmful microorganisms in the vagina.

• Bacterial vaginosis is a syndrome marked by dramatic shifts in the types

and relative proportions of the vaginal microbiota as the vaginal ecosystem
changes from a healthy to a diseased state.
Distribution and Occurrence of normal flora
• We are going to study
1. Flora on Skin
2. Flora in Eye/Conjunctiva
3. Oral microbiome project
4. Flora in mouth
5. Normal flora of nose, nasopharynx and accessory sinuses
6. normal flora in GI tract
7. normal flora in Genitourinary tract
8. normal flora in Blood and Tissues
Distribution and Occurrence of normal flora in skin
• The flora depends on area of the body (different anatomic areas by
secretions or proximity to mucous membranes), the clothing one wears,
ones occupation and environment
• Penicillin resistant Streptococci are seen in people working in hospitals
• Hair frequently harbors S. aureus and forms a reservoir for cross infection
• Fact - Neither profuse sweating nor washing and bathing can eliminate or
significantly modify the normal resident flora.
• The number of superficial microorganisms may be diminished by vigorous
daily scrubbing with soap containing hexachlorophene or other
disinfectants,
• The flora is rapidly replenished from sebaceous and sweat glands
 Skin is an immunological barrier

• Keratinocytes continuously sample the microbiota colonizing the skin

surface through pattern recognition receptors (eg, Toll-like receptors,
mannose receptors, NOD-like receptors).
• The activation of keratinocyte pattern recognition receptors by
pathogen-associated molecular patterns initiates the innate immune
response, resulting in the secretion of antimicrobial peptides,
cytokines, and chemokines.
• Despite being constantly exposed to large numbers of
microorganisms, the skin can distinguish between harmless
commensals and harmful pathogenic microorganisms. The
mechanism for this selectivity is unclear.
List of skin microflora
• Staphylococcus epidermidis
• Staphylococcus aureus (in small numbers)
• Micrococcus species α-Hemolytic and nonhemolytic streptococci (eg,
Streptococcus mitis)
• Corynebacterium species
• Propionibacterium species
• Peptostreptococcus species
• Acinetobacter species
• Small numbers of other organisms (Candida species, Pseudomonas
aeruginosa, etc)
 Distribution and Occurrence of normal flora in
Eye/Conjuntiva
• The predominant organisms of the conjunctiva are diphtheroids, S
epidermidis, and nonhemolytic streptococci.
• Neisseriae and gram-negative bacilli resembling haemophili
(Moraxella species) are also frequently present.
• The conjunctival flora is normally held in check by the flow of tears,
which contain antibacterial lysozyme.
 Oral microbiome project
• The human oral microbiome, as represented by the human salivary
microbiome, has recently been characterized in samples obtained
from 120 healthy individuals from 12 worldwide locations by 16S
rRNA sequencing.
• There is considerable diversity in the saliva microbiome, both within
and among individuals; however, it does not vary substantially around
the world.
• The 16S rRNA sequences could be assigned to 101 known bacterial
genera, of which 39 were not previously reported from the human
oral cavity;
• phylogenetic analysis suggests that an additional 64 unknown genera
are also present.
Distribution and Occurrence of normal flora in mouth
• Dental plaque, which has come to be viewed and managed as a
complex biofilm, can be defined simplistically as an adherent dental
deposit that forms on the tooth surface composed almost entirely of
bacteria derived from the normal flora of the mouth
Distribution and Occurrence of normal flora in mouth
and upper respiratory tract
Organ Organisms
Mouth Pigmented and non pigmented
Aerobic Gram positive spore bearing
bacilli, coliforms, Proteus spp and
Lactobacillus
Gum pockets between the teeth and Anaerobic micrococci, microaerophilic
crypts of tonsils and gingivae of adults and anaerobic streptococci, vibrios,
fusiform bacilli, Corynebacterium,
leptothrix, neisseria, mycoplasma,
Actinomycetes, Candida, geotrichum, etc
upper respiratory tract Alpha haemolytic streptococci
Pharynx and trachea Normal flora similar to mouth
Bronchi Normal flora similar to mouth
(lesser in number)
Smaller bronchi and alveoli Usually sterile
Distribution and Occurrence of normal flora in mouth
• Infections of the mouth and respiratory tract are usually caused by
mixed oronasal flora, including anaerobes.
• Periodontal infections, perioral abscesses, sinusitis, and mastoiditis
may involve predominantly P melaninogenica, Fusobacteria, and
Peptostreptococci.
• Aspiration of saliva (containing up to 102 of these organism) may
result in necrotizing pneumonia, lung abscess, and empyema.
 Normal flora of nose, nasopharynx and
accessory sinuses
• The nasopharynx can be considered as natural habitat of common
pathogens causing infection of nose, throat, bronchi and lungs
• Certain Gram negative organisms from intestinal tract are also
occasionally found in normal person (after penicillin therapy)
Microflora of nasopharynx
Any amount of the following:
• diphtheroids,
• nonpathogenic Neisseria species,
• α-hemolytic streptococci,
• S. epidermidis,
• nonhemolytic streptococci,
• anaerobes (too many species to list; varying amounts of Prevotella species, anaerobic
cocci, Fusobacterium species, etc)
Lesser amounts of the following when accompanied by organisms listed above:
• yeasts,
• Haemophilus species,
• pneumococci,
• S. aureus,
• Gram negative rods,
• Neisseria meningitidis
Distribution and Occurrence of normal flora in GI tract
• Diet has a marked influence on the relative composition of intestinal
and fecal flora
• The microorganisms on surface are those swallowed from saliva and
mouth
• Stomach is sterile due to low pH (except immediately after eating)
• Patients suffering from carcinoma, achlorhydria and pyrolic
obstruction harbour Gram positive cocci
• Number of bacteria increases beyond duodenum to colon
• In duodenum and upper ileum lactobacilli and enterococci
predominate while the lower ileum and cecum he flora resembles the
fecal flora
List of GI tract and rectum microflora
• Various Enterobacteriaceae except Salmonella, Shigella, Yersinia,
Vibrio, and Campylobacter species
• Glucose non-fermenting gram-negative rods Enterococci
• α-Hemolytic and nonhemolytic streptococci
• Diphtheroids
• Staphylococcus aureus in small numbers
• Yeasts in small numbers
• Anaerobes in large numbers (too many species to list)
 Distribution and Occurrence of normal flora in
Genitourinary tract
• The female urethra is either sterile or contains a few Gram positive
cocci. From men, aerobic and anaerobic bacteria can be cultured
• During pregnanacy, there is increase in Staphylococcus epidermidis,
Doderlien’s bacilli and yeast
• Occasionally other members of intestinal flora may be present
• After menopause, the flora resembles that found before puberty
Distribution and Occurrence of normal flora in urethra

• The anterior urethras of both sexes contain small numbers of the

same types of organisms found on the skin and perineum.
• These organisms regularly appear in normal voided urine in numbers
of 102–104/mL.
 List of organisms of genitalia

Any amount of the following:

• Mycobacterium smegmatis, Corynebacterium species, Lactobacillus
species, α-hemolytic and nonhemolytic streptococci, non pathogenic
Neisseria species
The following not predominant
• Enterococci, Enterobacteriaceae and other gram-negative rods,
Staphylococcus epidermidis, Candida albicans, and other yeasts as
well as anaerobes (too many to list)
Distribution and Occurrence of normal flora in Blood and
Tissues
• The commensals from normal flora of the mouth, nasopharynx and
intestinal tract may get into blood and tissues

• They are immediately eliminated by normal defense mechanism

• Occasional isolation of diphtheroids or non hemolytic streptococci

from normal and abnormal lymph nodes may be those that escaped
elimination
Definitions
• Once established, the normal microbiota can benefit the host by preventing
the overgrowth of harmful microorganisms. This phenomenon is called
microbial antagonism, or competitive exclusion
• The relationship between the normal microbiota and the host illustrates
symbiosis, a relationship between two organisms in which at least one
organism is dependent on the other
• In the symbiotic relationship called commensalism, one of the organisms
benefits, and the other is unaffected. Many of the microorganisms that
make up our normal microbiota are commensals
• Mutualism is a type of symbiosis that benefits both organisms. For
example, the large intestine contains bacteria, such as E. coli, that
synthesize vitamin K and some B vitamins.
Definitions
• One organism benefits by deriving nutrients at the expense of the other;
this relationship is called parasitism. Many disease-causing bacteria are
parasites.

• Opportunistic organisms are the organisms that don’t cause disease in

their normal habitat in a healthy person but may do so in a different
environment; or, if the host is already weakened or compromised by
infection, microbes that are usually harmless can cause disease.

For example,
1. microbes that gain access through broken skin or mucous membranes can
cause opportunistic infections
2. For example AIDS is often accompanied by a common opportunistic
infection, Pneumocystis pneumonia, caused by the opportunistic organism
Pneumococcus jirovecii
Significance of normal microflora of human body

• In environment laden with pathogens

1. Hospitals – Microbiota shift is observed. Increased in carriage of
antibiotic resistant staphylococci is observed

1. Army camps – the new recruit experience increased colonization by

Neisseria, Group A Streptococcus and some viruses
 Signs, symptoms and syndrome
Sign Physician can observe
•• Lesions
•• Edema
•• Fever
•• paralysis

Symptoms Not apparent to an observer

•• Pain
•• Malaise

A specific group of symptoms or signs may always accompany a

particular disease; such a group is called a syndrome.
CLASSIFICATION OF INFECTIOUS DISEEASES
Behavior within a host and
within a given population Infectious Disease State of host
communicable
disease Primary
non communicable Secondary
disease

Contagious

Extent of host
Severity of Disease involvement
Frequency of Occurrence
localized disease
of Disease Chronic disease
sporadic disease systemic disease
Acute disease
Epidemic disease Focal infections
Sub acute disease
endemic disease
Latent disease
Pandemic disease
Behavior within the host/ population
• A communicable disease is a disease in which an infected person transmits
an infectious agent, either directly or indirectly, to another person who in
turn becomes infected. pneumonia

• Chickenpox, measles, influenza, genital herpes, typhoid fever, and

tuberculosis are examples. Chickenpox and measles are also examples of
contagious diseases,
• Contagious disease is a very communicable and capable of spreading easily
and rapidly from one person to another. Conjunctivitis

• A noncommunicable disease does not spread from one host to another.

These diseases are caused by microorganisms that normally inhabit the
body and only occasionally produce disease or by microorganisms that
reside outside the body and produce disease only when introduced into the
body. Malaria

• An example is tetanus: Clostridium tetani produces disease only when it is

introduced into the body via abrasions or wounds.
 Occurrence of disease
• The incidence of a disease is the number of people in a population who
develop a disease during a particular time period
• It is an indicator of spread of disease
• The prevalence of a disease is the number of people in a population who
develop a disease at a specified time, regardless of when it first appeared.
• Prevalence takes into account both old and new cases. It’s an indicator of
how seriously and how long a disease affects a population.
• It is an indicator of how seriously and how long a disease affects a
population
• These parameters enable scientists to estimate the range of the disease’s
occurrence and its tendency to affect some groups of people more than
others
 Frequency of occurrence
• If a particular disease occurs only occasionally, it is called a sporadic
disease; typhoid fever in the United States is such a disease. Conjunctivitis,
Malaria

• A disease constantly present in a population is called an endemic disease;

an example of such a disease is the common cold. Penumonia, STDs

• If many people in a given area acquire a certain disease in a relatively short

period, it is called an epidemic disease; influenza is an example of a disease
that often achieves epidemic status. Cholera

• An epidemic disease that occurs worldwide is called a pandemic disease.

We experience pandemics of influenza from time to time.
 Severity/duration of the disease
• An acute disease is one that develops rapidly but lasts only a short time; a
good example is influenza.
• A chronic disease develops more slowly. Infectious mononucleosis,
tuberculosis, and hepatitis B fall into this category.
• A disease that is intermediate between acute and chronic is described as a
subacute disease. An example is subacute sclerosing panencephalitis, a
rare brain disease characterized by diminished intellectual function and loss
of nervous function.
• A latent disease is one in which the causative agent remains inactive for a
time but then becomes active to produce symptoms of the disease; an
example is shingles, one of the diseases caused by Varicello virus. The virus
can enter nerves and remain latent (dormant). Later, changes in the
immune response can activate the virus, causing shingles. TB, Typhoid

• Another example of a latent disease is cold sores, which are caused by

Simplex virus. The virus resides in the nerve cells of the body but causes no
damage until it is activated by a stimulus such as sunburn or fever.
 Herd immunity
• Immune individuals act as a barrier to the spread of infectious agents.
• Even though a highly communicable disease may cause an epidemic, many
nonimmune people will be protected because of the unlikelihood of their
coming into contact with an infected person.
• A great advantage of vaccination is that it protects enough individuals in a
population to prevent the disease’s rapid spread to those in the population
who aren’t vaccinated.
• If most people in a population (herd) are immune to a particular disease,
this form of immunity is referred to as herd immunity.
• Where there is herd immunity, outbreaks are limited to sporadic cases
because there are not enough susceptible individuals to support the spread
of the disease to epidemic proportions.
• Susceptible individuals include children who are too young to be vaccinated
or whose parents refuse to vaccinate them, people with immune disorders,
and those who are too ill to be vaccinated
Extent of host involvement
• A local infection is one in which the invading microorganisms are
limited to a relatively small area of the body. For example of boils and
abscesses. Vaginosis, acne,
fungal infection

• In a systemic (generalized) infection, microorganisms or their

products are spread throughout the body by the blood or lymph.
TB, typhoid,
Measles is an example of a systemic infection. shigellosis

• Very often, agents of a local infection enter a blood or lymphatic

vessel and spread to other specific parts of the body, where they are
confined to specific areas of the body. This condition is called a focal
infection. Focal infections can arise from infections in areas such as
the teeth, tonsils, or sinuses. Ulcers
 State of host
• A primary infection is an acute infection that causes the initial illness.
• A secondary infection is one caused by an opportunistic pathogen
after the primary infection has weakened the body’s defenses.
• Secondary infections of the skin and respiratory tract are common
and are sometimes more dangerous than the primary infections.
• Pneumocystis pneumonia as a consequence of AIDS is an example of
a secondary infection (causative agent for HW) Pnemocystis jirovecii

• Streptococcal bronchopneumonia following influenza is an example of

a secondary infection that is more serious than the primary infection
(causative agent for HW) Streptococcus
pneumoniae

• A subclinical infection also called inapparent infection, is one that

doesn’t cause any noticeable illness. Poliovirus and hepatitis A virus,
for example, can be carried by people who never develop the illness.
 Some definitions

• Sepsis is a toxic inflammatory condition arising from the spread of

microbes, especially bacteria or their toxins, from a focus of infection.
• Septicemia, also called blood poisoning, is a systemic infection arising
from the multiplication of pathogens in the blood. Septicemia is a
common example of sepsis.
• The presence of bacteria in the blood is known as bacteremia.
• Toxemia refers to the presence of toxins in the blood (as occurs in
tetanus) Botulinum

• Viremia refers to the presence of viruses in blood.

Development of a disease
 Development of a disease
• Etiology-The cause, set of causes, or manner of causation of a disease
condition
• The incubation period is the interval between the initial infection and
the first appearance of any signs or symptoms
• The prodromal period is a relatively short period that follows the
period of incubation in some diseases. The prodromal period is
characterized by early, mild symptoms of disease, such as general
aches and malaise
• During the period of illness, the disease is most severe. The person
exhibits overt signs and symptoms of disease
• During the period of decline, the signs and symptoms subside.
• During the period of convalescence, the person regains strength and
the body returns to its pre diseased state
Spread of infection
 Reservoir of infection
• For a disease to perpetuate itself, there must be a continual source of
the disease organisms.
• This source can be either a living organism or an inanimate object
that provides a pathogen with adequate conditions for survival and
multiplication and an opportunity for transmission.
• Such a source is called a reservoir of infection.
• These reservoirs may be human, animal, or nonliving.
Reservoir of infection
 Reservoir of infection - Human
• The principal living reservoir of human disease is the human body
itself.
• Many people harbor pathogens and transmit them directly or
indirectly to others.
• People with signs and symptoms of a disease may transmit the
disease; in addition, some people can harbor pathogens and transmit
them to others without exhibiting any signs of illness.
• These people, called carriers, are important living reservoirs of
infection
 Reservoir of infection - Human
• For example, immune adolescents and adults carry Bordetella pertussis and
can transmit an infection to a nonvaccinated infant.
• Some carriers have inapparent infections for which no signs or symptoms
are ever exhibited.
• Other people, such as those with latent diseases, carry a disease during its
symptom-free stages— during the incubation period (before symptoms
appear) or during the convalescent period (recovery).
• Typhoid Mary is an example of a carrier
• Human carriers play an important role in the spread of such diseases as
diphtheria, typhoid fever, hepatitis, gonorrhea, amebic dysentery, and
streptococcal infections.
 Reservoir of infection - Animals
• Both wild and domestic animals are living reservoirs of
microorganisms that can cause human diseases.
• Diseases that occur primarily in wild and domestic animals and can be
transmitted to humans are called zoonoses (singular: zoonosis).
• Rabies (found in bats, skunks, foxes, dogs, and coyotes), and Lyme
disease (found in field mice) are examples of zoonoses
 Reservoir of infection - Animals
• About 150 zoonoses are known.
• Zoonoses can be transmitted to humans via one of many routes:
• by direct contact with infected animals;
• by direct contact with domestic pet waste (such as cleaning a litter
box or bird cage);
• by contamination of food and water;
• by air from contaminated hides, fur, or feathers;
• by consuming infected animal products; or
• by arthropod vectors (insects and ticks that transmit pathogens).
 Reservoir of infection – non living
• The two major nonliving reservoirs of infectious disease are soil and
water.
• Soil harbors such pathogens as fungi, which cause mycoses such as
ringworm and systemic infections;
• Clostridium botulinum, the bacterium that causes botulism; and C.
tetani, the bacterium that causes tetanus.
• Because both species of clostridia are part of the normal intestinal
microbiota of horses and cattle, the bacteria are found especially in
soil where animal feces are used as fertilizer.
 Reservoir of infection – non living
• Water that’s been contaminated by the feces of humans and other
animals is a reservoir for several pathogens, notably those responsible
for gastrointestinal diseases.
• These include Vibrio cholerae, which causes cholera;
• Cryptosporidium, one cause of diarrhea;
• and Salmonella typhi, which causes typhoid fever.
• Other nonliving reservoirs include foods that are improperly prepared
or stored.
• They may be sources of diseases such as trichinellosis and
salmonellosis.
Transmission of disease
 Transmission of
infection

Contact Vehicle Vector

Direct Airborne Mechanical

Congenital waterborne Biological

Indirect Foodborne

Droplet
 Transmission of disease
• Direct contact transmission, also known as person-to-person
transmission, is the direct transmission of an agent by physical
contact between its source and a susceptible host; no intermediate
object is involved
• The most common forms of direct contact transmission are touching,
kissing, and sexual intercourse.
• Among the diseases that can be transmitted by direct contact are viral
respiratory tract diseases (the common cold and influenza),
staphylococcal infections, hepatitis A, measles, scarlet fever, and
sexually transmitted infections (syphilis, gonorrhea, and genital
herpes).
 Transmission of disease
• Direct contact is also one way to spread AIDS, syphilis, and infectious
mononucleosis.
• To guard against person-to-person transmission, health care workers
use gloves and other protective measures
• Potential pathogens can also be transmitted by direct contact from
animals (or animal products) to humans.
• Examples are the pathogens causing rabies (direct contact via bites)
and anthrax
 Transmission of disease
• Congenital transmission is the transmission of diseases from mother
to fetus or newborn at birth.
• This occurs when a pathogen present in the mother’s blood is capable
of crossing the placenta or through direct contact with a pathogen in
the mother’s blood or vaginal secretions during delivery
 Transmission of disease
• Indirect contact transmission occurs when the agent of disease is
transmitted from its reservoir to a susceptible host by means of a
nonliving object.
• The general term for any nonliving object involved in the spread of an
infection is a fomite.
• Examples of fomites are stethoscopes, clothing from health care
personnel, tissues, handkerchiefs, towels, bedding, diapers, drinking
cups, eating utensils, toys, money, and thermometers.
• Contaminated syringes serve as fomites in transmitting AIDS and
hepatitis B.
• Other fomites may transmit diseases such as tetanus,
methicillin-resistant S. aureus (MRSA), and impetigo.
 Transmission of disease
• Droplet transmission is a third type of contact transmission in which
microbes are spread in droplet nuclei (mucus droplets) that travel only
short distances
• These droplets are discharged into the air by coughing, sneezing, laughing,
or talking and travel less than 1 meter from the reservoir to the host.
• One sneeze may produce 20,000 droplets.
• Disease agents that travel such short distances are not considered airborne
(airborne transmission is discussed shortly).
• Pathogens can travel at varying distances depending on the size and shape
of the particles, initial velocity (coughing, sneezing, or normal exhalation),
and environmental conditions such as humidity.
• Examples of diseases spread by droplet transmission are influenza,
pneumonia, and pertussis (whooping cough).
 Transmission of disease
• Vehicle transmission is the transmission of disease agents by a
medium, such as air, water, or food
• Other media include blood and other body fluids, drugs, and
intravenous fluids.
 Transmission of disease
• Airborne transmission refers to the spread of agents of infection by
droplet nuclei in dust that travel more than 1 meter from the
reservoir to the host.
• For example, microbes are spread by droplets, which may be
discharged in a fine spray from the mouth and nose during coughing
and sneezing
• These droplets are small enough to remain airborne for prolonged
periods.
• The virus that causes measles and the bacterium that causes
tuberculosis can be transmitted via airborne droplets.
 Transmission of disease
• Dust particles can harbor various pathogens.
• Staphylococci and streptococci can survive on dust and be
transmitted by the airborne route.
• Spores produced by certain fungi are also transmitted by the airborne
route and can cause such diseases as histoplasmosis,
coccidioidomycosis, and blastomycosis
 Transmission of disease
• In waterborne transmission, pathogens are usually spread by water
contaminated with untreated or poorly treated sewage.
• Diseases transmitted via this route include cholera, waterborne
shigellosis, and leptospirosis.
 Transmission of disease
• In foodborne transmission, pathogens are generally transmitted in
foods that are incompletely cooked, poorly refrigerated, or prepared
under unsanitary conditions.
• Foodborne pathogens cause diseases such as food poisoning and
tapeworm infestation.
• Foodborne transmission frequently occurs because of
cross-contamination, the transfer of pathogens from one food to
another.
• This can occur when pathogens on hands, gloves, knives, cutting
boards, countertops, utensils, and cooking equipment spread to food.
 Transmission of disease
• This takes place when pathogens on the surface of raw meat, poultry,
seafood, and vegetables and raw eggs are transferred to ready-to-eat
foods (foods that do not require cooking or have already been
cooked, such as salads and sandwiches).
• Cross-contamination is responsible for numerous cases of food
poisoning.
• Both waterborne and foodborne transmission also provide a transfer
of microbes by fecal-oral transmission.
 Transmission of disease
• In the cycle, some microbes are ingested contaminated in water or
food.
• The pathogens usually enter the water or food after being shed in the
feces of people or animals infected with them.
• The cycle is interrupted by effective sanitation practices in food
handling and production.
 Transmission of disease
• Arthropods are the most important group of disease vectors—
animals that carry pathogens from one host to another.
• Arthropod vectors transmit disease by two general methods.
• Mechanical transmission is the passive transport of the pathogens on
the insect’s feet or other body parts
• If the insect makes contact with a host’s food, pathogens can be
transferred to the food and later swallowed by the host.
• Houseflies, for instance, can transfer the pathogens of typhoid fever
and bacillary dysentery (shigellosis) from the feces of infected people
to food.
 Transmission of disease
• Biological transmission is an active process and is more complex.
• The arthropod bites an infected person or animal and ingests some of
the infected blood
• The pathogens then reproduce in the vector, and the increase in the
number of pathogens increases the possibility that they will be
transmitted to another host.
• Some parasites reproduce in the gut of the arthropod; these can be
passed with feces.
 Transmission of disease
• If the arthropod defecates or vomits while biting a potential host, the
parasite can enter the wound.
• Other parasites reproduce in the vector’s gut and migrate to the
salivary gland; these are directly injected into a bite.
• Some protozoan and helminthic parasites use the vector as a host for
a developmental stage in their life cycle
 Nosocomial
• Healthcare-associated infections (HAIs) are infections patients acquire
while receiving treatment for other conditions at a health care facility,
such as a nursing home, hospital, same-day surgery center, outpatient
clinic, or in-home health care environment.
• Traditionally these were called nosocomial infections (nosocomial is
Latin for hospital).
• HAIs result from the interaction of several factors:
(1) microorganisms in the hospital environment,
(2) the compromised (or weakened) status of the host, and
(3) the chain of transmission in the hospital
 Nosocomial- microorganisms in the hospital
environment
• Although every effort is made to kill or check the growth of
microorganisms in the hospital, the hospital environment is a major
reservoir for a variety of pathogens.
• One reason is that certain normal microbiota of the human body are
opportunistic and present a particularly strong danger to hospital
patients.
• In fact, most of the microbes that cause HAIs don’t cause disease in
healthy people but are pathogenic only for individuals whose
defenses have been weakened by illness or therapy
 Nosocomial- microorganisms in the hospital
environment
• Staphylococcus aureus is the primary cause of most of the HAIs.
• In the 1970s, gram-negative rods, such as E. coli and Pseudomonas
aeruginosa, were the most common causes of HAIs.
• Then, during the 1980s, antibiotic resistant gram-positive
bacteria—Staphylococcus aureus, coagulase negative staphylococci
and Enterococcus spp.— emerged as healthcare-associated
pathogens.
• Clostridium difficile (causes Diarrhea after abdominal surgery) is now
the leading cause of HAIs
• P. aeruginosa and other such gram-negative bacteria tend to be
difficult to control with antibiotics because of their R factors, which
carry genes that determine resistance to antibiotics
 Nosocomial-Compromised host
• A compromised host is one whose resistance to infection is impaired
by disease, therapy, or burns.
• Two principal conditions can compromise the host: broken skin or
mucous membranes, and a suppressed immune system.
• Burns, surgical wounds, trauma (such as accidental wounds),
injections, invasive diagnostic procedures, ventilators, intravenous
therapy, and urinary catheters (used to drain urine) can all break the
first line of defense and make a person more susceptible to disease in
hospitals.
• The risk of infection is also related to other invasive procedures, such
as administering anesthesia, which may alter breathing and
contribute to pneumonia, and tracheotomy, in which an incision is
made into the trachea to assist breathing.
 Nosocomial-Compromised host
• The risk of infection is also related to other invasive procedures, such
as administering anesthesia, which may alter breathing and
contribute to pneumonia, and tracheotomy, in which an incision is
made into the trachea to assist breathing.
• Drugs, radiation therapy, steroid therapy, burns, diabetes, leukemia,
kidney disease, stress, and malnutrition can all adversely affect the
actions of T and B cells and compromise the host.
• In addition, the AIDS virus destroys certain T cells.
 Nosocomial-Chain of transmission
• Given the variety of pathogens (and potential pathogens) in health
care settings and the compromised state of the host, routes of
transmission are a constant concern.
• The principal routes of transmission of HAIs are
(1) direct contact - transmission from hospital staff to patient and from
patient to patient and
(2) indirect contact - transmission through fomites and the hospital’s
ventilation system (airborne transmission).
 Nosocomial-Chain of transmission
• Many diagnostic and therapeutic hospital procedures provide a
fomite route of transmission.
• The urinary catheter used to drain urine from the urinary bladder is a
fomite in many HAIs.
• Intravenous catheters, which pass through the skin and into a vein to
provide fluids, nutrients, or medication, can also transmit HAIs.
• Respiratory aids can introduce contaminated fluids into the lungs.
• Needles may introduce pathogens into muscle or blood, and surgical
dressings can become contaminated and promote disease
 Nosocomial-Control
• Universal precautions are employed to reduce the transmission of
microbes in health care and residential settings
• The various precautions can be grouped into two general categories:
standard precautions and transmission-based precautions.
 Nosocomial-Control
• Standard precautions-
• These are basic, minimum practices designed to prevent transmission
of pathogens from one person to another and are applied to every
person every time.
• They are employed at all levels of health care, regardless of whether a
patient’s infection status is confirmed, suspected, or unknown.
• Among the standard precautions are hand hygiene, use of personal
protective equipment (gloves, gowns, facemasks), respiratory hygiene
and cough etiquette, disinfection of patient-care equipment and
instruments, environmental cleaning and disinfection, safe injection
practices, patient placement, and safe resuscitation and lumbar
puncture procedures
 Nosocomial-Control
• Transmission-based precautions are procedures designed to
supplement standard precautions in individuals with known or
suspected infections that are highly transmissible or epidemiologically
important pathogens.
• They are employed when standard precautions do not completely
interrupt the transmission route.
• There are three categories of transmission-based precautions:
contact, droplet, and airborne.
 Nosocomial-Control
• Accredited hospitals should have an infection control committee.
• Most hospitals have at least an infection control nurse or
epidemiologist (an individual who studies disease in populations).
• The role of these staff members is to identify problem sources, such
as antibiotic-resistant strains of bacteria and improper sterilization
techniques.
• The infection control officer should make periodic examinations of
hospital equipment to determine the extent of microbial
contamination.
• Samples should be taken from tubing, catheters, respirator reservoirs,
and other equipment.
Laboratory Diagnostic techniques
The clinical specimen should-
1. Adequately represent the diseased area and may include additional sites (e.g.,
urine and blood specimens) to isolate and identify potential agents of the
particular disease process.
2. Be of sufficient quality and quantity to allow a variety of diagnostic testing,
should they be necessary.
3. Avoid contamination from the many varieties of microorganisms indigenous to
the skin, mucous membranes, and environment.
4. Be collected in appropriate containers, kept at an appropriate temperature, and
forwarded promptly to the clinical laboratory.
5. Be obtained before antimicrobial agents have been administered to the patient,
if possible.
6. Be accompanied by a putative diagnosis permitting laboratory personnel to
contact the physician suggesting tests necessary to "rule out" other pathogens.
Identification of pathogen (infecting agent) based on

• the direct recovery of the infectious agent from the clinical specimen

• the indirect evidence that a specific pathogen was the likely source of
the infection
Direct Identification of Infectious Agents
• Culture based method

• Microscopy

• Molecular methods
Culture based methods
• These tests vary, depending on whether the suspected organism is
virus, fungi (yeasts, molds), parasite (protozoa, helminths), or
Gram-positive or Gram-negative bacteria (including rickettsias,
chlamydiae, or mycoplasmas).
• The initial identity of a bacterial organism may be suggested by
1. The source of the specimen
2. Its pattern of growth on selective, differential, or metabolism
-determining media
3. Its hemolytic, metabolic, and fermentative properties on the
various media
• Once isolated in pure culture, growth characteristics of the bacterium
are examined and specific biochemical tests are performed.
 Miniaturization into kits and robotic automation
• Some smaller laboratories use a "kit approach" biochemical system,
e.g. API 20E (identification of members of the family
Enterobacteriaceae and other Gram-negative bacteria)
• Larger laboratories also use semiautomated robotic systems to detect
microorganisms.
e.g. the VITEK 2 automated microbiology system, the Versa TREK, and
the MicroScan WalkAway
• These systems use reagents and reporting components that are
uniquely made for them
• Colorimetric or fluorometric reactions resulting from each test are
evaluated against controls to report on the specific capabilities of the
organism
 Microscopy
• Wet-mount
• Heat-fixed
• Chemically fixed specimens
Can be examined with an ordinary bright-field microscope.
Examination can be enhanced with either phase-contrast or darkfield
microscopy, found in some laboratories.
The fluorescence microscope can be used to identify any
microorganism after it is stained with fluorochromes such as acridine
orange
Direct immunofluorescence involves fixing the specimen containing
the antigen of interest onto a slide
Molecular biology
• The most accurate and sensitive methods for the identification of
microorganisms are those that report their presence through the
analysis of proteins and nucleic acids
1. nucleic acid probes
2. real-time PCR amplification of DNA
3. DNA fingerprinting
4. Ribotyping
5. Multilocus sequence typing (MLST)
Indirect Identification of Infectious Agents

• Test based on immune responses

 Clinical Immunology
• Serotyping
• Agglutination
• Complement Fixation
• Enzyme-Linked lmmunosorbent Assay
• lmmunoblotting (Western Blotting)
• Immunoprecipitation
• Immunodiffusion
• Immunoelectrophoresis
• Flow Cytometry
• Radioimmunoassay
 Laboratory information system
1. Outpatient samples may be received with barcodes or with
paperwork that must be entered into the laboratory information
system (LIS).
2. The LIS prints barcodes to be affixed to the outpatient specimens.
3. A barcode reader attached to the LIS interfaces automated testing
machines to request tests.
4. The LIS tracks the testing process and manages the test results.
5. Test results and their interpretation typically identify a specific
infectious agent and report on its antimicrobial sensitivities (when
appropriate).
6. The LIS data are accessible directly to the other hospital
departments, reducing the time in which results are delivered to
the clinical staff attending the patient.
Biosafety
Events that have led to the formation of laws

• The recognition that the human immunodeficiency virus (HIV) and

other viruses were transmitted by blood led to the 1991 Bloodborne
Pathogens Act

• The use of anthrax as a bioterrorism agent led to the Public Health

Security and Bioterrorism Preparedness and Response Act of 2002

• The response to emerging viruses with high infectivity or high

lethality (such as SARS and avian influenza) resulted in the 2005
Pandemic and All-Hazards Preparedness Act
Portal of entry
• Pathogens can gain entrance to the human body and other hosts
through several avenues, which are called portals of entry.
• The portals of entry for pathogens are mucous membranes, skin, and
direct deposition beneath the skin or membranes (the parenteral
route).
Portal of entry- mucous membrane
• Many bacteria and viruses gain access to the body by penetrating
mucous membranes lining the
1. respiratory tract,
2. gastrointestinal tract,
3. genitourinary tract, and
4. conjunctiva, a delicate membrane that covers the eyeballs and lines
the eyelids.
• Most pathogens enter through the mucous membranes of the
gastrointestinal and respiratory tracts.
Portal of entry- Respiratory tract mucous
membrane
• Microbes are inhaled into the nose or mouth in drops of moisture and
dust particles.
• Diseases that are commonly contracted via the respiratory tract
include the common cold, pneumonia, tuberculosis, influenza, and
measles
Portal of entry- Gastrointestinal tract
• Microbes in the gastrointestinal tract can cause poliomyelitis,
hepatitis A, typhoid fever, amoebic dysentery, giardiasis, shigellosis
(bacillary dysentery), and cholera.
• These pathogens are then eliminated with feaces and can be
transmitted to other hosts via contaminated water, food, or fingers.
Portal of entry- Genitourinary tract
• The genitourinary tract is a portal of entry for pathogens that are
contracted sexually.
• Some microbes that cause sexually transmitted infections (STIs) may
penetrate an unbroken mucous membrane.
• Others require a cut or abrasion of some type.
• Examples of STIs are HIV infection, genital warts, chlamydia, human
herpesvirus-2, syphilis, and gonorrhea.
Portal of entry- Skin
• The conjunctiva is a delicate mucous membrane that lines the eyelids
and covers the white of the eyeballs.
• Although it is a relatively effective barrier against infection, certain
diseases such as conjunctivitis, trachoma, and ophthalmia
neonatorum are acquired through the conjunctiva.
Portal of entry- Skin
• The skin is the largest organ of the body, in terms of surface area and
weight, and is an important defense against disease.
• Unbroken skin is impenetrable by most microorganisms.
• Some microbes gain access to the body through openings in the skin,
such as hair follicles and sweat gland ducts.
• Larvae of the hookworm actually bore through intact skin, and some
fungi grow on the keratin in skin or infect the skin itself.
Portal of entry- Parenteral route
• Other microorganisms gain access to the body when they are deposited
directly into the tissues beneath the skin or into mucous membranes when
these barriers are penetrated or injured.
• This route is called the parenteral route.
• Punctures, injections, bites, cuts, wounds, surgery, and splitting of the skin
or mucous membrane due to swelling or drying can all establish parenteral
routes.
• HIV, the hepatitis viruses, and bacteria that cause tetanus and gangrene can
be transmitted parenterally.
• Even after microorganisms have entered the body, they do not necessarily
cause disease.
• The occurrence of disease depends on several factors, only one of which is
the portal of entry.
Preferred portal of entry
• Many pathogens have a preferred portal of entry that is a prerequisite
to their being able to cause disease.
• If they gain access to the body by another portal, disease might not
occur. Eg. Study from Tortora
 Number of invading organism
• If only a few microbes enter the body, they will probably be overcome
by the host’s defenses.
• However, if large numbers of microbes gain entry, the stage is
probably set for disease.
• The likelihood of disease increases as the number of pathogens
increases.
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 Number of invading organism
• The virulence of a microbe is often expressed as the ID50 (infectious
dose for 50% of a sample population).
• The 50 is not an absolute value; rather, it is used to compare relative
virulence under experimental conditions.
• Bacillus anthracis can cause infection via three different portals of
entry.
• The ID50 through the skin (cutaneous anthrax) is 10 to 50 endospores;
the ID50 for inhalation anthrax is inhalation of 10,000 to 20,000
endospores; and the ID50 for gastrointestinal anthrax is ingestion of
250,000 to 1,000,000 endospores.
 Number of invading organism
• These data show that cutaneous anthrax is significantly easier to
acquire than either the inhalation or the gastrointestinal forms
• A study of Vibrio cholerae showed that the ID50 is 108 cells; but if
stomach acid is neutralized with bicarbonate, the number of cells
required to cause an infection decreases significantly.
 Number of invading organism
• The potency of a toxin is often expressed as the LD50 (lethal dose for
50% of a sample population).
• For example, the LD50 for botulinum toxin in mice is 0.03 ng/kg; for
Shiga toxin, 250 ng/kg; and staphylococcal enterotoxin, 1350 ng/kg.
• In other words, compared to the other two toxins, a much smaller
dose of botulinum toxin is needed to cause symptoms.
 Adherence
• Almost all pathogens have some means of attaching themselves to
host tissues at their portal of entry.
• For most pathogens, this attachment, called adherence (or adhesion),
is a necessary step in pathogenicity. (Of course, nonpathogens also
have structures for attachment.)
• The attachment between pathogen and host is accomplished by
means of surface molecules on the pathogen called adhesins or
ligands that bind specifically to complementary surface receptors on
the cells of certain host tissues
• Adhesins may be located on a microbe’s glycocalyx or on other
microbial surface structures, such as pili, fimbriae, and flagella
Adherence
 Adherence
• The majority of adhesins on the microorganisms studied so far are
glycoproteins or lipoproteins.
• The receptors on host cells are typically sugars, such as mannose.
• Adhesins on different strains of the same species of pathogen can
vary in structure.
• Different cells of the same host can also have different receptors that
vary in structure.
• If adhesins, receptors, or both can be altered to interfere with
adherence, infection can often be prevented (or at least controlled).
• Microbes have the ability to come together in masses, cling to
surfaces, and take in and share available nutrients in communities
called biofilms
 Adherence
• Study example from Tortora
 How bacteria penetrate host defenses?
• Although some pathogens can cause damage on the surface of
tissues, most must penetrate tissues to cause disease.
 How bacteria penetrate host defenses?
Capsule Enzymes Antigenic variation

Some
pathogens can alter their surface
antigens, by a process called
antigenic variation.
These chemicals can digest
capsule resists the host’s defenses materials between cells and form or
By the time the body mounts an
by impairing phagocytosis digest blood clots, among other
immune response against a
functions.
pathogen, the pathogen has already
altered its antigens and is
unaffected by the antibodies.
 How bacteria penetrate host defenses?
Biofilms Penetration into host

Microbes attach to host cells by adhesins.

The interaction triggers signals in the host cell that
activate factors that can result in the entrance of
Biofilms also play a role in evading phagocytes.
some bacteria.
The actual mechanism is provided by the host cell
Bacteria that are part of biofilms are much more
cytoskeleton.
resistant to phagocytosis.
The microfilaments of the eukaryotic cytoskeleton are
composed of a protein called actin, which is used by
Phagocytes do not move through the viscous
some microbes to penetrate host cells and by others
carbohydrates of the extracellular polymeric
to move through and between host cells.
substance (EPS) of biofilms
 How bacteria penetrate host defenses?
• Study example from Tortora
 How bacteria damage host cells?
• When a microorganism invades a body tissue, it initially encounters
phagocytes of the host.
• If the phagocytes are successful in destroying the invader, no further
damage is done to the host.
• But if the pathogen overcomes the host’s defense, then the
microorganism can damage host cells in four basic ways-
 How bacteria damage host cells?
1. By using the host’s nutrients.
2. By causing direct damage in the immediate vicinity of the invasion.
3. By producing toxins, transported by blood and lymph, that damage
sites far removed from the original site of invasion.
4. By inducing hypersensitivity reactions
 How bacteria damage host cells?
Using the Host’s Nutrients: Siderophores
• Iron is required for the growth of most pathogenic bacteria.
• Iron is required for the growth of most pathogenic bacteria.
• However, the concentration of free iron in the human body is fairly
low because most of the iron is tightly bound to iron-transport
proteins, such as lactoferrin, transferrin, and ferritin, as well as
hemoglobin.
• Siderophores are released by some pathogens, they take the iron
away from iron-transport proteins by binding the iron even more
tightly
• Also, it is possible that some bacteria produce toxins when iron levels
are low. The toxins kill host cells, releasing their iron and thereby
making it available to the bacteria.
 How bacteria damage host cells?
Direct Damage
• Once pathogens attach to host cells, they can cause direct damage as
the pathogens use the host cell for nutrients and produce waste
products.
• As pathogens metabolize and multiply in cells, the cells usually
rupture.
• Many viruses and some intracellular bacteria and protozoa that grow
in host cells are released when the host cell ruptures.
• Following their release, pathogens that rupture cells can spread to
other tissues in even greater numbers.
• Some bacteria, such as E. coli, Shigella, Salmonella, and Neisseria
gonorrhoeae, can induce host epithelial cells to engulf them by a
process that resembles phagocytosis
 How bacteria damage host cells?
Direct Damage
• These pathogens can disrupt host cells as they pass through and can
then be extruded from the host cells by exocytosis, enabling them to
enter other host cells.
• Some bacteria can also penetrate host cells by excreting enzymes or
by their own motility; such penetration can itself damage the host
cell.
• Most damage by bacteria, however, is done by toxins.
 How bacteria damage host cells?
Toxin
• Toxins are poisonous substances that are produced by certain
microorganisms.
• They are often the primary factor contributing to the pathogenic
properties of those microbes.
• The capacity of microorganisms to produce toxins is called
toxigenicity. Toxins transported by the blood or lymph can cause
serious, and sometimes fatal, effects.
• Some toxins produce fever, cardiovascular disturbances, diarrhea, and
shock.
 How bacteria damage host cells?
Toxin
• Toxins can also inhibit protein synthesis, destroy blood cells and blood
vessels, and disrupt the nervous system by causing spasms.
• The term toxemia refers to the presence of toxins in the blood.
• Toxins are of two general types, based on their position relative to the
microbial cell: exotoxins and endotoxins.
• Intoxications are caused by the presence of a toxin; not by microbial
growth.
 How bacteria damage host cells?
Exotoxin
• Exotoxins are produced inside some bacteria (mostly gram negative)
as part of their growth and metabolism and are secreted by the
bacterium into the surrounding medium or released following lysis
How bacteria damage host cells?
 How bacteria damage host cells?
Exotoxin
• Diseases caused by bacteria that produce exotoxins are often caused
by minute amounts of exotoxins, not by the bacteria themselves.
• It is the exotoxins that produce the specific signs and symptoms of the
disease.
• Thus, exotoxins are disease-specific. For example, botulism is usually
due to ingestion of the exotoxin, not to a bacterial infection.
• Likewise, staphylococcal food poisoning is an intoxication, not an
infection.
 How bacteria damage host cells?
Exotoxin
• The body produces antibodies called antitoxins that provide immunity
to exotoxins.
• When exotoxins are inactivated by heat or by formaldehyde, iodine,
or other chemicals, they no longer cause the disease but can still
stimulate the body to produce antitoxins.
• Such altered exotoxins are called toxoids.
• When toxoids are injected into the body as a vaccine, they stimulate
antitoxin production so that immunity is produced.
• Diphtheria and tetanus can be prevented by toxoid vaccination.
 How bacteria damage host cells?
Types of Exotoxins
• Exotoxins are divided into three principal types on the basis of their
structure and function:
(1) A-B toxins,
(2) membrane-disrupting toxins, and
(3) superantigens.
 How bacteria damage host cells?
Types of Exotoxins
(1) A-B toxins - The A part is the active (enzyme) component, and the B
part is the binding component
(2) membrane-disrupting toxins - cause lysis of host cells by disrupting
their plasma membranes.
Some do this by forming protein channels in the plasma membrane;
others disrupt the phospholipid portion of the membrane
(3) Superantigens - Superantigens are antigens that provoke a very
intense immune response.
They are bacterial proteins that combine with a protein on
macrophages; this nonspecifically stimulates the proliferation of T cells.
 How bacteria damage host cells?
Endotoxins
These are part of the outer portion of the cell wall of gram-negative
bacteria
Outer membrane consists of lipoproteins, phospholipids, and
lipopolysaccharides (LPS)
The lipid portion of LPS, called lipid A, is the endotoxin
 How bacteria damage host cells?
Endotoxins
All endotoxins produce the same signs and symptoms, regardless of the
species of microorganism, although not to the same degree.
These include chills, fever, weakness, generalized aches, and, in some
cases, shock and even death.
Endotoxins can also induce miscarriage.
How bacteria damage host cells?
 Endotoxins
• It is important to have a sensitive test to identify the presence of
endotoxins in drugs, medical devices, and body fluids.
• Materials that have been sterilized may contain endotoxins, even
though no bacteria can be cultured from them.
• One such laboratory test is called the Limulus amebocyte lysate (LAL)
assay, which can detect even minute amounts of endotoxin.
• The hemolymph (blood) of the Atlantic coast horseshoe crab, Limulus
polyphemus, contains white blood cells called amebocytes, which
have large amounts of a protein (lysate) that causes clotting.
• In the presence of endotoxin, amebocytes in the crab hemolymph
lyse and liberate their clotting protein.
• The resulting gel-clot (precipitate) is a positive test for the presence of
endotoxin.
• The degree of the reaction is measured using a spectrophotometer
Spread of infection
 Reservoir of infection
• For a disease to perpetuate itself, there must be a continual source of
the disease organisms.
• This source can be either a living organism or an inanimate object
that provides a pathogen with adequate conditions for survival and
multiplication and an opportunity for transmission.
• Such a source is called a reservoir of infection.
• These reservoirs may be human, animal, or nonliving.
Reservoir of infection
 Reservoir of infection - Human
• The principal living reservoir of human disease is the human body
itself.
• Many people harbor pathogens and transmit them directly or
indirectly to others.
• People with signs and symptoms of a disease may transmit the
disease; in addition, some people can harbor pathogens and transmit
them to others without exhibiting any signs of illness.
• These people, called carriers, are important living reservoirs of
infection
 Reservoir of infection - Human
• For example, immune adolescents and adults carry Bordetella
pertussis and can transmit an infection to a nonvaccinated infant.
• Some carriers have inapparent infections for which no signs or
symptoms are ever exhibited.
• Other people, such as those with latent diseases, carry a disease
during its symptom-free stages— during the incubation period
(before symptoms appear) or during the convalescent period
(recovery).
• Typhoid Mary is an example of a carrier
• Human carriers play an important role in the spread of such diseases
as diphtheria, typhoid fever, hepatitis, gonorrhea, amebic dysentery,
and streptococcal infections.
 Reservoir of infection - Animals
• Both wild and domestic animals are living reservoirs of
microorganisms that can cause human diseases.
• Diseases that occur primarily in wild and domestic animals and can be
transmitted to humans are called zoonoses (singular: zoonosis).
• Rabies (found in bats, skunks, foxes, dogs, and coyotes), and Lyme
disease (found in field mice) are examples of zoonoses
 Reservoir of infection - Animals
• About 150 zoonoses are known.
• Zoonoses can be transmitted to humans via one of many routes:
• by direct contact with infected animals;
• by direct contact with domestic pet waste (such as cleaning a litter
box or bird cage);
• by contamination of food and water;
• by air from contaminated hides, fur, or feathers;
• by consuming infected animal products; or
• by arthropod vectors (insects and ticks that transmit pathogens).
 Reservoir of infection – non living
• The two major nonliving reservoirs of infectious disease are soil and
water.
• Soil harbors such pathogens as fungi, which cause mycoses such as
ringworm and systemic infections;
• Clostridium botulinum, the bacterium that causes botulism; and C.
tetani, the bacterium that causes tetanus.
• Because both species of clostridia are part of the normal intestinal
microbiota of horses and cattle, the bacteria are found especially in
soil where animal feces are used as fertilizer.
 Reservoir of infection – non living
• Water that’s been contaminated by the feces of humans and other
animals is a reservoir for several pathogens, notably those responsible
for gastrointestinal diseases.
• These include Vibrio cholerae, which causes cholera;
• Cryptosporidium, one cause of diarrhea;
• and Salmonella typhi, which causes typhoid fever.
• Other nonliving reservoirs include foods that are improperly prepared
or stored.
• They may be sources of diseases such as trichinellosis and
salmonellosis.
Transmission of disease
 Transmission of
infection

Contact Vehicle Vector

Direct Airborne Mechanical

Congenital waterborne Biological

Indirect Foodborne

Droplet
 Transmission of disease
• Direct contact transmission, also known as person-to-person
transmission, is the direct transmission of an agent by physical
contact between its source and a susceptible host; no intermediate
object is involved
• The most common forms of direct contact transmission are touching,
kissing, and sexual intercourse.
• Among the diseases that can be transmitted by direct contact are viral
respiratory tract diseases (the common cold and influenza),
staphylococcal infections, hepatitis A, measles, scarlet fever, and
sexually transmitted infections (syphilis, gonorrhea, and genital
herpes).
 Transmission of disease
• Direct contact is also one way to spread AIDS, syphilis, and infectious
mononucleosis.
• To guard against person-to-person transmission, health care workers
use gloves and other protective measures
• Potential pathogens can also be transmitted by direct contact from
animals (or animal products) to humans.
• Examples are the pathogens causing rabies (direct contact via bites)
and anthrax
 Transmission of disease
• Congenital transmission is the transmission of diseases from mother
to fetus or newborn at birth.
• This occurs when a pathogen present in the mother’s blood is capable
of crossing the placenta or through direct contact with a pathogen in
the mother’s blood or vaginal secretions during delivery
 Transmission of disease
• Indirect contact transmission occurs when the agent of disease is
transmitted from its reservoir to a susceptible host by means of a
nonliving object.
• The general term for any nonliving object involved in the spread of an
infection is a fomite.
• Examples of fomites are stethoscopes, clothing from health care
personnel, tissues, handkerchiefs, towels, bedding, diapers, drinking
cups, eating utensils, toys, money, and thermometers.
• Contaminated syringes serve as fomites in transmitting AIDS and
hepatitis B.
• Other fomites may transmit diseases such as tetanus,
methicillin-resistant S. aureus (MRSA), and impetigo.
 Transmission of disease
• Droplet transmission is a third type of contact transmission in which
microbes are spread in droplet nuclei (mucus droplets) that travel
only short distances
• These droplets are discharged into the air by coughing, sneezing,
laughing, or talking and travel less than 1 meter from the reservoir to
the host.
• One sneeze may produce 20,000 droplets.
• Disease agents that travel such short distances are not considered
airborne (airborne transmission is discussed shortly).
• Pathogens can travel at varying distances depending on the size and
shape of the particles, initial velocity (coughing, sneezing, or normal
exhalation), and environmental conditions such as humidity.
• Examples of diseases spread by droplet transmission are influenza,
pneumonia, and pertussis (whooping cough).
 Transmission of disease
• Vehicle transmission is the transmission of disease agents by a
medium, such as air, water, or food
• Other media include blood and other body fluids, drugs, and
intravenous fluids.
 Transmission of disease
• Airborne transmission refers to the spread of agents of infection by
droplet nuclei in dust that travel more than 1 meter from the
reservoir to the host.
• For example, microbes are spread by droplets, which may be
discharged in a fine spray from the mouth and nose during coughing
and sneezing
• These droplets are small enough to remain airborne for prolonged
periods.
• The virus that causes measles and the bacterium that causes
tuberculosis can be transmitted via airborne droplets.
 Transmission of disease
• Dust particles can harbor various pathogens.
• Staphylococci and streptococci can survive on dust and be
transmitted by the airborne route.
• Spores produced by certain fungi are also transmitted by the airborne
route and can cause such diseases as histoplasmosis,
coccidioidomycosis, and blastomycosis
 Transmission of disease
• In waterborne transmission, pathogens are usually spread by water
contaminated with untreated or poorly treated sewage.
• Diseases transmitted via this route include cholera, waterborne
shigellosis, and leptospirosis.
 Transmission of disease
• In foodborne transmission, pathogens are generally transmitted in
foods that are incompletely cooked, poorly refrigerated, or prepared
under unsanitary conditions.
• Foodborne pathogens cause diseases such as food poisoning and
tapeworm infestation.
• Foodborne transmission frequently occurs because of
cross-contamination, the transfer of pathogens from one food to
another.
• This can occur when pathogens on hands, gloves, knives, cutting
boards, countertops, utensils, and cooking equipment spread to food.
 Transmission of disease
• This takes place when pathogens on the surface of raw meat, poultry,
seafood, and vegetables and raw eggs are transferred to ready-to-eat
foods (foods that do not require cooking or have already been
cooked, such as salads and sandwiches).
• Cross-contamination is responsible for numerous cases of food
poisoning.
• Both waterborne and foodborne transmission also provide a transfer
of microbes by fecal-oral transmission.
 Transmission of disease
• In the cycle, some microbes are ingested contaminated in water or
food.
• The pathogens usually enter the water or food after being shed in the
feces of people or animals infected with them.
• The cycle is interrupted by effective sanitation practices in food
handling and production.
 Transmission of disease
• Arthropods are the most important group of disease vectors—
animals that carry pathogens from one host to another.
• Arthropod vectors transmit disease by two general methods.
• Mechanical transmission is the passive transport of the pathogens on
the insect’s feet or other body parts
• If the insect makes contact with a host’s food, pathogens can be
transferred to the food and later swallowed by the host.
• Houseflies, for instance, can transfer the pathogens of typhoid fever
and bacillary dysentery (shigellosis) from the feces of infected people
to food.
 Transmission of disease
• Biological transmission is an active process and is more complex.
• The arthropod bites an infected person or animal and ingests some of
the infected blood
• The pathogens then reproduce in the vector, and the increase in the
number of pathogens increases the possibility that they will be
transmitted to another host.
• Some parasites reproduce in the gut of the arthropod; these can be
passed with feces.
 Transmission of disease
• If the arthropod defecates or vomits while biting a potential host, the
parasite can enter the wound.
• Other parasites reproduce in the vector’s gut and migrate to the
salivary gland; these are directly injected into a bite.
• Some protozoan and helminthic parasites use the vector as a host for
a developmental stage in their life cycle
 Nosocomial
• Healthcare-associated infections (HAIs) are infections patients acquire
while receiving treatment for other conditions at a health care facility,
such as a nursing home, hospital, same-day surgery center, outpatient
clinic, or in-home health care environment.
• Traditionally these were called nosocomial infections (nosocomial is
Latin for hospital).
• HAIs result from the interaction of several factors:
(1) microorganisms in the hospital environment,
(2) the compromised (or weakened) status of the host, and
(3) the chain of transmission in the hospital
 Nosocomial- microorganisms in the hospital
environment
• Although every effort is made to kill or check the growth of
microorganisms in the hospital, the hospital environment is a major
reservoir for a variety of pathogens.
• One reason is that certain normal microbiota of the human body are
opportunistic and present a particularly strong danger to hospital
patients.
• In fact, most of the microbes that cause HAIs don’t cause disease in
healthy people but are pathogenic only for individuals whose
defenses have been weakened by illness or therapy
 Nosocomial- microorganisms in the hospital
environment
• Staphylococcus aureus is the primary cause of most of the HAIs.
• In the 1970s, gram-negative rods, such as E. coli and Pseudomonas
aeruginosa, were the most common causes of HAIs.
• Then, during the 1980s, antibiotic resistant gram-positive
bacteria—Staphylococcus aureus, coagulase negative staphylococci
and Enterococcus spp.— emerged as healthcare-associated
pathogens.
• Clostridium difficile (causes Diarrhea after abdominal surgery) is now
the leading cause of HAIs
• P. aeruginosa and other such gram-negative bacteria tend to be
difficult to control with antibiotics because of their R factors, which
carry genes that determine resistance to antibiotics
 Nosocomial-Compromised host
• A compromised host is one whose resistance to infection is impaired
by disease, therapy, or burns.
• Two principal conditions can compromise the host: broken skin or
mucous membranes, and a suppressed immune system.
• Burns, surgical wounds, trauma (such as accidental wounds),
injections, invasive diagnostic procedures, ventilators, intravenous
therapy, and urinary catheters (used to drain urine) can all break the
first line of defense and make a person more susceptible to disease in
hospitals.
• The risk of infection is also related to other invasive procedures, such
as administering anesthesia, which may alter breathing and
contribute to pneumonia, and tracheotomy, in which an incision is
made into the trachea to assist breathing.
 Nosocomial-Compromised host
• The risk of infection is also related to other invasive procedures, such
as administering anesthesia, which may alter breathing and
contribute to pneumonia, and tracheotomy, in which an incision is
made into the trachea to assist breathing.
• Drugs, radiation therapy, steroid therapy, burns, diabetes, leukemia,
kidney disease, stress, and malnutrition can all adversely affect the
actions of T and B cells and compromise the host.
• In addition, the AIDS virus destroys certain T cells.
 Nosocomial-Chain of transmission
• Given the variety of pathogens (and potential pathogens) in health
care settings and the compromised state of the host, routes of
transmission are a constant concern.
• The principal routes of transmission of HAIs are
(1) direct contact - transmission from hospital staff to patient and from
patient to patient and
(2) indirect contact - transmission through fomites and the hospital’s
ventilation system (airborne transmission).
 Nosocomial-Chain of transmission
• Many diagnostic and therapeutic hospital procedures provide a
fomite route of transmission.
• The urinary catheter used to drain urine from the urinary bladder is a
fomite in many HAIs.
• Intravenous catheters, which pass through the skin and into a vein to
provide fluids, nutrients, or medication, can also transmit HAIs.
• Respiratory aids can introduce contaminated fluids into the lungs.
• Needles may introduce pathogens into muscle or blood, and surgical
dressings can become contaminated and promote disease
 Nosocomial-Control
• Universal precautions are employed to reduce the transmission of
microbes in health care and residential settings
• The various precautions can be grouped into two general categories:
standard precautions and transmission-based precautions.
 Nosocomial-Control
• Standard precautions-
• These are basic, minimum practices designed to prevent transmission
of pathogens from one person to another and are applied to every
person every time.
• They are employed at all levels of health care, regardless of whether a
patient’s infection status is confirmed, suspected, or unknown.
• Among the standard precautions are hand hygiene, use of personal
protective equipment (gloves, gowns, facemasks), respiratory hygiene
and cough etiquette, disinfection of patient-care equipment and
instruments, environmental cleaning and disinfection, safe injection
practices, patient placement, and safe resuscitation and lumbar
puncture procedures
 Nosocomial-Control
• Transmission-based precautions are procedures designed to
supplement standard precautions in individuals with known or
suspected infections that are highly transmissible or epidemiologically
important pathogens.
• They are employed when standard precautions do not completely
interrupt the transmission route.
• There are three categories of transmission-based precautions:
contact, droplet, and airborne.
 Nosocomial-Control
• Accredited hospitals should have an infection control committee.
• Most hospitals have at least an infection control nurse or
epidemiologist (an individual who studies disease in populations).
• The role of these staff members is to identify problem sources, such
as antibiotic-resistant strains of bacteria and improper sterilization
techniques.
• The infection control officer should make periodic examinations of
hospital equipment to determine the extent of microbial
contamination.
• Samples should be taken from tubing, catheters, respirator reservoirs,
and other equipment.
Laboratory Diagnostic techniques
The clinical specimen should-
1. Adequately represent the diseased area and may include additional sites (e.g.,
urine and blood specimens) to isolate and identify potential agents of the
particular disease process.
2. Be of sufficient quality and quantity to allow a variety of diagnostic testing,
should they be necessary.
3. Avoid contamination from the many varieties of microorganisms indigenous to
the skin, mucous membranes, and environment.
4. Be collected in appropriate containers, kept at an appropriate temperature, and
forwarded promptly to the clinical laboratory.
5. Be obtained before antimicrobial agents have been administered to the patient,
if possible.
6. Be accompanied by a putative diagnosis permitting laboratory personnel to
contact the physician suggesting tests necessary to "rule out" other pathogens.
Identification of pathogen (infecting agent) based on

• the direct recovery of the infectious agent from the clinical specimen

• the indirect evidence that a specific pathogen was the likely source of
the infection
Direct Identification of Infectious Agents
• Culture based method

• Microscopy

• Molecular methods
Culture based methods
• These tests vary, depending on whether the suspected organism is
virus, fungi (yeasts, molds), parasite (protozoa, helminths), or
Gram-positive or Gram-negative bacteria (including rickettsias,
chlamydiae, or mycoplasmas).
• The initial identity of a bacterial organism may be suggested by
1. The source of the specimen
2. Its pattern of growth on selective, differential, or metabolism
-determining media
3. Its hemolytic, metabolic, and fermentative properties on the
various media
• Once isolated in pure culture, growth characteristics of the bacterium
are examined and specific biochemical tests are performed.
 Miniaturization into kits and robotic automation
• Some smaller laboratories use a "kit approach" biochemical system,
e.g. API 20E (identification of members of the family
Enterobacteriaceae and other Gram-negative bacteria)
• Larger laboratories also use semiautomated robotic systems to detect
microorganisms.
e.g. the VITEK 2 automated microbiology system, the Versa TREK, and
the MicroScan WalkAway
• These systems use reagents and reporting components that are
uniquely made for them
• Colorimetric or fluorometric reactions resulting from each test are
evaluated against controls to report on the specific capabilities of the
organism
 Microscopy
• Wet-mount
• Heat-fixed
• Chemically fixed specimens
Can be examined with an ordinary bright-field microscope.
Examination can be enhanced with either phase-contrast or darkfield
microscopy, found in some laboratories.
The fluorescence microscope can be used to identify any
microorganism after it is stained with fluorochromes such as acridine
orange
Direct immunofluorescence involves fixing the specimen containing
the antigen of interest onto a slide
Molecular biology
• The most accurate and sensitive methods for the identification of
microorganisms are those that report their presence through the
analysis of proteins and nucleic acids
1. nucleic acid probes
2. real-time PCR amplification of DNA
3. DNA fingerprinting
4. Ribotyping
5. Multilocus sequence typing (MLST)
Indirect Identification of Infectious Agents

• Test based on immune responses

 Clinical Immunology
• Serotyping
• Agglutination
• Complement Fixation
• Enzyme-Linked lmmunosorbent Assay
• lmmunoblotting (Western Blotting)
• Immunoprecipitation
• Immunodiffusion
• Immunoelectrophoresis
• Flow Cytometry
• Radioimmunoassay
 Laboratory information system
1. Outpatient samples may be received with barcodes or with
paperwork that must be entered into the laboratory information
system (LIS).
2. The LIS prints barcodes to be affixed to the outpatient specimens.
3. A barcode reader attached to the LIS interfaces automated testing
machines to request tests.
4. The LIS tracks the testing process and manages the test results.
5. Test results and their interpretation typically identify a specific
infectious agent and report on its antimicrobial sensitivities (when
appropriate).
6. The LIS data are accessible directly to the other hospital
departments, reducing the time in which results are delivered to
the clinical staff attending the patient.
Biosafety
Events that have led to the formation of laws

• The recognition that the human immunodeficiency virus (HIV) and

other viruses were transmitted by blood led to the 1991 Bloodborne
Pathogens Act

• The use of anthrax as a bioterrorism agent led to the Public Health

Security and Bioterrorism Preparedness and Response Act of 2002

• The response to emerging viruses with high infectivity or high

lethality (such as SARS and avian influenza) resulted in the 2005
Pandemic and All-Hazards Preparedness Act