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Normal Microbiota :
.

Affecting pH and available oxygen Competing for nutrients

Protect the host by

Producing substances harmful to invading microbes

Human Microbiome Begins to established in utero

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become the predominant organisms

Remain throughout life in the newborn’s intestine
* Notes
- The placental microbiome consists of only few different bacteria, mostly :
Enterobacteriaceae and Propionibacterium.

- More microorganisms acquired from food, people, and pets

- Two types of birth

Vaginal birth Cesareanbirthas

prevalently Lactobacillus and Bacteroides Staphylococcus aureus
- microbiome resembles
the human skin
 Advantages of Normal microbiota : -

Development of immune system .

production of vitamins ( Bandk) .

Interfere with colonization
of primary pathogens .

By
competitive exclusions

competing producing substances Affecting

for nutrients .
harmfulto microbes .
pltandoz .

Disadvantages of Normal microbiota : -

Weakingorcollapseoftheimmune Translocation intoasterilebodysite Overgrowth of some members

system Hader, kidney bloodstream lungs of normal flora during antibiotic

( peritoneal cavity muscle )
.
> ,

,
CNS, . administration .

microbes that can disease

④ primary pathogens 8 cause .

④ secondary pathogens
oomicrobotiathatcan cause disease .

( opportunistic pathogens) ex : c. difficile .

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Development of immune system .
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 Antibiotics Physical and
Age chemical factors
physiological changes associated with human age affect microbiota

Mechanical factors Distribution and composition of Nutrients

normal microbiota are food habits of individuals or
determined by many factors communities

Host defenses
can be affected by genetic mutations that affect :
The immune system, age, AIDS, cancer, chemotherapy, diabetes, immunosuppressive drugs.

Prebiotics Probiotics

Definition Nonliving , nondigestible special Live active microorganisms that when

from of fiber or carbohydrates administered in adequate amount will
have beneficial effects to its host

Resistance The powder form of prebiotics More fragile , Vulnerable to heat

can survive heat, cold, and acid Maybe killed over time

Function Nourishing the bacteria that live in Fight the harmful bacterial species
the intestines present in the gut
i. Unbalanced gutmicrobotiatl £* 86.14*0 • Unbalanced microbotiajl b↳*

① ②

② ②

③ ③

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The immune system keeps normalfloraincheak -8GW -

skin saliva and tears Themucosaofdigestivetract

secrete : secrete :
secretes :

Sweatandcertainfattyacids .
↳sosyme Antibodies (IgA) and antibiotic peptides
that :
thats thats

limit bacterial growth kills bacteria limit bacterial growth

(inhibitory substances) .
( by destroying peptidoglycan .
 Representative Normal Microbiota by Body Region

it
secretions from Way of acting

Skin - sweat & oil glands have antimicrobial properties.

has (relatively low - Keratin a resistant barrier
moisture content.)
- low pH of the skin inhibits many microbes. So
Most of the microties In direct contact with skin don't become residents

Eyes (Conjunctiva) - Tears and blinking eliminate some microbes or inhibit others from
contains basically the same colonizing.
microbtota found on the skin

Nose and Throat - Nasal secretions kill or inhibit many microbes

(Upper Respiratory - mucus and ciliary action remove many microbes.
System

Mouth - Biting, chewing, tongue flow dislodge microbes

movements, and salivary
- Saliva contains several antimicrobial substances.

Large intestine - Mucus produces several antimicrobial chemicals.

contains the largest numbers of - periodic shedding of the lining prevent many microbes from attaching to the lining of
resident microbiota in the body
because of its available moisture the gastrointestinal tract
and nutrients

Urinary & - Mucus & periodic shedding of the prevent microbes from attaching to the
Reproductive lining lining
Systems - urine flow removes microbes
The lower urethra in both
- pH of urine and urea antimicrobial
sexes has a resident
population: the vagina has - acidity of the vagina inhibits or kills microbes.
an acid-tolerant - Cilia and mucus expel microbes from the cervix of the uterus into the
population of microbes
vagina
because of the nature of its
secretions.

* ‫*تلخيص الجدول اللي فيه الكومنتس‬

 11

Microbiota beyond Bacteria 10 bacterial cells per gram'

111 j
Eukaryotic parasites &
Mycobiome Virome Archaeome
heleminths
5 6
10 to 10 fungal presence of over 15
15

The number 10 bacteriophages,

cells per gram of outnumbering the
different genera of
commensal bacteria by a
fecal matter factor of 10 protozoa

inhabits the In the intestine in the human known to parasitize, but

Function gastrointestinal tract being the most gastrointestinal also commensalize the
skin, respiratory tract, extensively human gastrointestinal tract
tract
genitourinary tract,
:other mucosal populated

surfaces in the host

Components Candida particularly C -Double-stranded DNA The majority is amoebozoans, flagellates, ciliates,
(dsDNA), methane-producing stramenopiles, and apicomplexans
-Single-stranded DNA organisms
(ssDNA), (methanogens).
- RNA viruses

Notes
* The human microbiota is a diverse microbial ecosystem associated with :
many beneficial physiological functions & numerous disease etiologies

* The microbiota includes commensal populations of fungi, viruses, archaea, and protists but
dominated by bacteria their functional roles, and their
interaction with one another or with
studied in the past two decades host immune system have not been as
widely explored
 Opportunistic diseases

Causing Notes

C. Difficile Antibiotic Associated Diarrhea mediated by Exotoxin A

Pseudomembranous colitis mediated by exotoxin B

Bacteroides Most causes: infections are usually endogenous ones

Peritonitis
Local abscesses at the site of a mucosal The infection may spread to distant
break on the colon organs through the blood steam

Streptococcus May cause: In most cases, infections caused by

pneumoniae Throat infection Streptococcus pneumomaeare
Bronchitis endogenous ones.
Pneumonia (typical pneumonia)
Septicemia and septic shock
Meningitis common cause of it among infants
Otitis media and Sinusitis common causeof of
Common cause among
otitis children
media among children

Enterobacteriacene Urinary tract infection when

Escherichia traveler’s diarrhea * overgrowth
Klebsielia Pneumonia * in immunocompromised

Entcrobacter Pneumonia
Serratia Pneumonia
Proteus

Candida albican Vaginitis, thrush, napkin diaper

candidiasis, blood stream infections

E.coli Urinary tract infection

=
 Koch’s Postulates

Analysis of the test :

- The same pathogen must be present in every case of the disease.
- The pathogen must be isolated from the diseased host and grown in pure culture.

Q: When the pathogen from the pure culture must cause the disease?
when it's inoculated into a healthy, susceptible laboratory animal.

- The pathogen must be isolated from the inoculated animal and must be shown to
be the original organism.

Q: What is the aim of the test ?

to prove the cause of an infectious disease

Q : Is Koch’s postulates successed?and why ?

Not at all there are exceptions:
- Some pathogens can cause several disease conditions
- Some pathogens cause disease only in humans
- Some microbes have never been cultured
 contact .

Transmission vehicle .

vectors .

Contact Transmission from to

-

Requires Notes :

Direct contact transmission -

person to person .
*
close association :
*

preventing itthroughuseofoo
touching Kissing gloves
-
-

. .
.

sexual intercourse masks

-

. .

Animal bites goggles

-
-

. .

congenital transmission from mother to

-

fetusornewbornat -
-

birth passes placenta .

Indirect contact transmission from nonliving

-

nonliving object
object toahost . Cfomite) . -

Droplet transmission viaairbronedropletkessthantmete.ro Mucus droplet

-

. .

less than Imeter coughing sneezing

-

. . .

Laughing talking
-
-

.
.

Vectors 81Arthropods; fleas >

ticks, lice, mosquitoes )
Transmit disease by : -

Mechanical transmission Biological transmission

Arthropod carries pathogen on pathogen repreducesinvector

its feet .
transmitted bybitesorfeces .
VehicleTransmission spread of pathogens by :

Airbrone -

dropletnudeiindustinorethantmeter
Ex : TB & measles
.

Waterbrone Water contaminated

-

Untreated or poorly treated sewage .

fecal-oral transmission
-

foodbrone Incompletely cooked food

-

poorly refrigerated food

-

prepared under unsanitary conditions

-

"
cross-contamination !fromonefoodtoanother
-

( pathogen onoohandgglovesgknives.it
fecal-oral transmission
-

④ fecal-oral transmission : -

Thepathogensenterfoodorwaterafterbeingshedinto
fecesofpeopleoranimalsinffectedwiththem .

itisintruptedbyoo effective sanitation particles infood handling

and production .

Ig
 Lack of vaccination
Fatigue Gender& Age

Chemotherapy Predisposing Factors

of a disease Climate and weather

Lifestyle Inherited traits, Nutrition

such as the sickle cell gene

Epidemiology
- What do Epidemiologists do ?
- Determine etiology of a disease
- Identify other important factors concerning the spread of disease
- Develop methods for controlling a disease
- Assemble data and graphs to outline incidence of a disease

- What does CDC means , what does it do?

Centers for Disease Control and Prevention
• Collects and analyzes epidemiological information in the United States
• Publishes Morbidity and Mortality Weekly Report (MMWR)

- Where do Blood cultures grow?

mannitol-salt agar; coagulase-positive; gram-positive cocci

- What are the two strains of Methicillin-resistant Staphylococcus aureus (MRSA)?

Strain USA100: 92% of Strain USA300: 89% of

healthcare strains community-acquired strains
 Reservoirs of Infection
Continual sources of infection

#
Human reservoirs Animal reservoirs Nonliving reservoirs

reservoirs Carriers Zoonoses Soil and water

Notes may have inapparent are diseases transmitted from

infections or latent animals to humans
diseases

Healthcare-Associated Infections (HAlS)

(nosocomial infections)
When ? The rate of infection
Acquired while receiving treatment Affect 1 in 25 hospital patients
in a health care facility - 2 million per year infected;
over 70,000 deaths

The causes?
- Microorganisms in the hospital environment
- Weakened status of the host
- Chain of transmission in a hospital

- What are the most principal Sites of Healthcare-

Associated Infections ?
Surgical site infections & Lower respiratory infections.
 - How to control of Healthcare-Associated Infections?

① Universal precautions

Standard precautions Transmission-based precautions

basic, minimum practices - supplemental to standard precautions
- designed for known or suspected
infections
■ Contact precautions
■ Droplet precautions
■ Airborne precautions

③
② Infection control
Reduce number of pathogens committees
- Handwashing
- Disinfecting tubs used to bathe patients
- Cleaning instruments scrupulously
- Using disposable bandages and intubation

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"‫سبَُلن َا‬ *ِ ‫"َوَما َلن َآ أ َ*) َنت ََو*كَل َعَلى ٱ‬
ُ ‫ َوَقْد َهَدٰىن َا‬4
 Emerging Infectious Diseases

Contributing factors Diseases/microbes Notes

Genetic recombination E.coli 0157: H7, Avian influenza

- New strains (H5N1)
Evolution of new strains Vibrio cholerae O139

Widespread use of Antibiotic-resistant strains

antibiotics &pesticides
Changes in Hantavirus May increase the : Distribution &
weather patterns survival of reservoirs and vectors

Introduction&dissemination of diseases
Modern Zika virus , Chikungunya
transportation West Nile encephalitis
Insect vectors mosquito (Aedes aegypti ) can transmit infections brought by
transported to new (came to the Americas with the human travelers.
areas first European explorers)
Ecological disaster Coccidioidomycosis Also war, and expanding human
settlement
Animal control Lyme disease may affect the incidence of a
measures killing of deer predators. disease
I
rising deer populations
The increase in incidence recent years

Failure of Public health Diphtheria epidemic in Soviet The cause :Adults who did not get a
measures Union in the 1990s. diphtheria booster vaccination

Bioterrorism

Most are zoonotic, of viral origin, and likely to be vector-borne

 ④ iw.jo#dl---.fd1I-i*o

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Microbe Classification Notes

Staphylococcus aureus Bacteria In the human skin

Lactobacillus & Bacteria In the Vaginae

Bacteroides
Candida (particularly C) (Fungi) Yeast The most common type of Mycobiome

Methanogens Archae

C. Difficile Bacteria Opportunistic disease ; causes Diarrhea &

Pseudomembranous colitis

Bacteroides Bacteria 1- are the predominant bacteria in the human

colon, of approximately 1011/gram of feces
2- causes Peritonitis & Local abscesses

Streptococcus Bacteria is an opportunistic pathogen that cause various

pneumoniae infections.

E.coli Bacteria Causes UTI, E. coli O157:H7 is a new strain

Vibrio cholerae O139 Bacteria Is an example of evaluation of new strains

Mosquito Insects The causative agent of Aedes aegypti

Coccidioidomycosis Fungi Spread by Ecological disaster

 l
Pathology the study of disease

Etiology the cause of a disease

Pathogenesis the development of disease

Infection invasion or colonization of the body by pathogens

Disease an abnormal state in which the body is not performing normal

functions

Symbiosis is the relationship between normal microbiota and the host

Commensalism one organism benefits, and the other is unaffected

Mutualism both organisms benefit

Parasitism one organism benefits at the expense of the other

Microbial antagonism is a competition between microbes

(competitive exclusion)

Human Microbiome Project analyzes relationships between microbial communities on the

body and humanhealth

Normal microbiota permanently colonize the host and do not cause disease under
normal conditions

Transient microbiota may be present for days, weeks,or months

 Bacteroides are the predominant bacteria in the human colon, of approximately
11
10/gram of feces

Streptococcus is an opportunistic pathogen that cause various infections

pneumoniae

Candida albican is a yeast and causes opportunistic infections in healthy persons

Symptoms changes in body function that are felt by a patient as a result of

disease

Signs changes in a body that can be measured or observed as a result

of disease

Syndrome a specific group of signs and symptoms that accompany a

disease

Communicable disease a disease that is spread from one host to another

Contagious diseases diseases that are easily and rapidly spread from one host to
another

Noncommunicable disease a disease that is not spread from one host to another

Incidence number of people who develop a disease during a particular

time period

Prevalence number of people who develop a disease at a specified time,

regardless of when it first appeared
- Takes into account both old and new cases
 Sporadic disease disease that occurs only occasionally

Endemic disease disease constantly present in a population

Epidemic disease disease acquired by many people in a given area in a short time

Pandemic disease worldwide epidemic

Acute disease symptoms develop rapidly but the disease lasts only a short
time

Chronic disease symptoms develop slowly

Subacute disease intermediate between acute and chronic

Latent disease causative agent is inactive for a time butthen activates and
produces symptoms

Herd immunity immunity in most of a population

Local infection pathogens are limited to a small area of the body

Systemic (generalized) infection an infection throughout the body

Focal infection systemic infection that began as a local infection

Sepsis toxic inflammatory condition arising from the spread of

microbes, especially bacteria or their toxins, from a focus of
infection

Bacteremia
bacteria in the blood
 Septicemia also known as blood poisoning; growth of bacteria in the blood

Toxemia toxins in the blood

Viremia viruses in the blood

Primary infection acute infection that causes the initial illness

Secondary infection opportunistic infection after a primary (predisposing) infection

Subclinical disease no noticeable signs or symptoms (inapparent infection)

Predisposing Factors Make the body more susceptible to disease

Incubation period interval between initial infection and first signs and symptoms

Prodromal period short period after incubation; early, mild symptoms

Period of illness disease is most severe

Period of decline signs and symptoms subside

Period of convalescence body returns to its prediseased state

Compromised host an individual whose resistance to infection is impaired by

disease, therapy, or burns

Emerging Infectious Diseases Diseases that are new, increasing in incidence, or showing a
potential to increase in the near future
 l
Epidemiology The study of where and when diseases occur and how they are
transmitted in populations

Morbidity incidence of a specific notifiable disease

Mortality deaths from notifiable diseases

Notifiable infectious diseases diseases in which physicians are required to report occurrence

Morbidity rate number of people affected in relation to the total population in a

given time period

Mortality rate number of deaths from a disease in relation to the population

in a given time

Vehicle Transmission Transmission by an inanimate reservoir (Vehicle transmission is

the transmission of disease agents by a medium)

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