This document discusses different types of bacteria including cocci and bacilli. It provides details on: 1) Gram positive cocci including Staphylococci which are further divided based on coagulase production into Staph. aureus and coagulase negative species. Streptococci are also discussed including S. pyogenes and S. pneumoniae. 2) Gram negative cocci including Neisseria with details on N. gonorrhoeae which causes gonorrhea and N. meningitidis which causes meningitis. 3) Selected gram positive bacilli such as Corynebacterium diphtheriae, Bacillus anthracis, and Clo

1. Cocci
Classification of cocci:
A) Gram positive:
Staphylococci and
Streptococci.
B) Gram negative:
Neisseria.

2. Gram Positive Cocci
1. Staphylococci
Morphology:
Staphylococci are Gram-positive cocci, arranged in
grape like clusters
Normal habitat:
Staphylococci usually inhabit the skin and mucosa.
They form part of normal flora of the skin, upper
respiratory tract and intestinal tract.
Classification: divided into two groups
according to the presence or absence of coagulase
enzyme:
Coagulase positive: only S. aureus.
Coagulase negative: all other species.

3. Staph. aureus (the most important & the more
pathogenic specie).
- Staph. Epidermidis.
- Staph. saprophyticus.
Staph. Epidermidis & Staph. Saprophyticus
are coagulase negative & are usually commensals
(skin).

4. Staphylococcus aureus
S. aureus is a major human pathogen.
May present as normal flora on the skin and
upper respiratory tract.
Pathogenicity:
S. aureus causes suppurative infections and
toxigenic diseases in humans.
1. Suppurative (pus-forming) infections:
- Localized skin infections as: abscess, post-
operative surgical wound infections, traumatic
wound infections following skin injury or burn.
- Pneumonia, urinary tract infections.
- Invasive infections: bacteremia, meningitis,
osteomyelitis &endocarditis.
2. Toxigenic diseases:
- Scalded skin syndrome in neonates.
- Food poisoning. - Toxic shock syndrome

5. 3. Hospital acquired (nosocomial)
infections.
Laboratory Diagnosis of S. aureus:
1- Samples: differ according to the clinical
site of infection, may be swabs, pus,
sputum, C.S.F, blood). Samples will be
examined by:
2-Direct film: Stained with Gram stain for
characteristic morphology.
3- Culture: • Staphylococci can be grown
on ordinary media at 37oc.
• On blood agar S. aureus cause -
hemolysis.
• On nutrient agar S. aureus produce
golden yellow endopigment.

6. 4- Biochemical reaction: S. aureus is catalase
positive & coagulase positive.
► Principle of catalase test:
Staphylococci produce catalase enzyme which breaks
down hydrogen peroxide to oxygen and water
leading to immediate bubbling in positive results.
► Principle of Coagulase test:
Staphylococci produce coagulase enzyme which
causes plasma to clot by converting fibrinogen to
fibrin

7. 2. Streptococci
Morphology:
Gram positive cocci arranged in long chains (S. pyogenes) or in
pairs (S. pneumoniae), non-motile, non-spore forming, some
species are capsulated.
Streptococcus pyogenes
Pathogenicity: Infections can be divided into:-
I) Diseases due to local infection.
II) Diseases due to invasion.
III) Post-streptococcal infection.
I) Diseases due to local infection:
a) Suppurative infections:
1. Respiratory infections: tonsillitis, sinusitis, otitis media and
pneumonia.
2. Skin infections: cellulitis.
b) Toxigenic diseases:
- Scarlet fever: fever, skin rash and stomatitis (Strawberry
tongue).

8. II) Invasive diseases:
a) Suppurative infections: Bacteremia,
osteomyelitis ,arthritis, meningitis
b) Toxigenic diseases: Streptococcal toxic shock
like syndrome.
III) Post streptococcal sequelae:
1) Acute rheumatic fever:
It is the most serious complication of
streptococcal pyogenes infection, as it leads to
damage of heart muscles and valves. In it a
streptococci contain a cell membrane protein that
act as an antigen and stimulate the immune
system to produce antibodies. These antibodies
then react with the human heart muscles.
2) Acute glomerulonephritis.

9. Laboratory Diagnosis of S. pyogenes:
a. Samples: differs according to the clinical
presentation.
b. Direct film: stained with Gram stain for
characteristic morphology.
c. Culture: S. pyogenes grow on blood agar
causes haemolysis.
d. Biochemical reaction:
- Catalase test: negative (differentiates them
from staphylococci).

10. Diagnosis of rheumatic fever:
a. Non-specific tests: as C- reactive protein
(CRP) and high ESR.
b. Specific tests: by detection of an increase
in anti-streptolysin O (A.S.O) titer with
diagnostic titre 200 todd's unit.

11. Streptococcus pneumoniae
Morphology: Gram positive diplococci,
capsulated, non-motile and non-spore forming.
Culture characters: Facultative anaerobes,
grow at 37oC. Cannot grow on ordinary media,
grow on blood agar producing haemolysis.
Growth is enhanced by 5-10% Co2.
Pathogenicity: S. pneumoniae is the most
frequent cause of pneumonia &its complications
as bacteremia, meningitis, septic arthritis
&endocarditis.
Diagnosis of pneumococcal infection:
Specimens: Sputum which is examined as follow:
1- Stained smears by Gram to detect the
morphology of the organism.
2- Capsule swelling test: fresh sputum is mixed
with antiserum.

12. Gram-Negative Cocci
Neisseria
Morphology:
Gram-negative cocci arranged in pairs
(diplococci) inside and outside pus cells,
non-motile, non-spore forming, some
species (N. meningitides) are capsulated.
Normal habitate:
Many of the members in the genus
Neisseria occur as commensals in the
mouth, pharynx and vagina and occur
extracellular.
Two members N. meningitidis & N.

13. Cultural characters:
N. gonorrhoea and N. meningitidis cannot grow on
ordinary culture media
they require enriched media for growth as blood agar
and chocolate agar. Cultures are incubated at 37C in
presence of 5-10% CO2 for 48 hours
Pathogenicity:
I) N. gonorrhoeae causes:
a) Venereal gonorrhoea:-
It is a venereal disease transmitted by sexual
intercourse, affects both males and females.
- Male: Acute urethritis with purulent urethral discharge
and painful urination (dysuria). The infection may
become chronic and complicated by urethral stricture,
prostatitis.
- Female: acute urethritis with dysuria and cervicitis
with mucopurulent vaginal discharge. It may extend to
fallobian tubes causing salpingitis, fibrosis and

14. b) Non venereal gonorrhoea:
- Ophthalmia neonatorum: An eye infection of
the newborn acquired from the birth canal of
gonorrhoeal mother.
- Purulent conjunctivitis in adults: The spread
of infection by the use of common towels or by
flies, self- infection from urethra may also occur.
II) N. meningitidis: causes acute cereprospinal
meningitis.
It is a highly contagious disease usually occurs in
epidemics among young adults. The organism
occurs in the nasopharynx of healthy carriers.
The infection is transmitted by droplets from
cases or carriers

15. it starts in the nasopharynx where it may remain
silent or gives rise to mild naso-pharyngitis. From
the nasopharynx, the organism may invade the
blood stream causing high fever, bad general
condition. The organism reaches the meninges via
the lymphatic or through the blood stream, causing
meningitis manifested by fever, sever headache,
vomiting and rigidity of the neck and back muscles.

16. Diagnosis of gonorrhea:
1-Specimen:
I) In acute cases :
- Urethral discharge from infected males .
- Urethral, vaginal or cervical discharges from infected
females.
II) In chronic cases :
- Morning drop from infected males.
- Cervical discharge from infected females .
2-Direct microscopic examination: smear stained
by gram show gram negative diplococci intracellular &
extracellular in pus cells is diagnostic.
3-Culture: on chocolate agar in presence of 5-10%
CO2.
3- Biochemical reactions: oxidase positive, catalase
positive.

17. Diagnosis of cereprospinal
meningitis:
1) Diagnosis of a case:
1-Specimen: CSF is withdrawn by lumbar
puncture under complete aseptic technique.
2-Direct microscopic examination: smear
stained by gram show gram negative
diplococci intracellular & extracellular in pus
cells is diagnostic.
3-Culture: on chocolate agar in presence of
5-10% CO2.
4- Biochemical reactions: oxidase
positive, catalase positive.
4- Serology: Slide agglutination with anti-
meningococcal sera.

18. Gram positive bacilli
Corynebacterium diphtheria
Morphology:
Gram positive bacilli, arranged in Chineese-letter
appearance, non-motile, non-capsulated & non-
spore forming.
Culture characters:
Aerobes, do not grow on ordinary media, grow on
enriched media called Loffler’s serum at 37C.
Pathogenesis:
C. Diphtheriae causes a disease called diphtheria
which is an upper respiratory tract illness
transmitted by droplet infection and characterized
by sore throat, low grade fever and an adherent
pseudo-membrane on the tonsils and pharynx. In it
Diphtheria bacilli do not invade tissues below the
site of the local lesion but they produce a powerful

19. Laboratory diagnosis:
1. Samples: swabs from the membrane.
2. Direct smears stained with Gram stain to
show the morphology.
3. Culture: isolated on Loeffler's serum
medium.
4. Toxigenicity tests (virulence tests):
It is essential to detect toxin production from
C. diphtheriae strains by:
a. In vivo virulence test in guinea pigs.
b. In vitro virulence test: (Elek's test).

20. Immunizaion against Diphtheria:
A- Active immunization:
Toxoid vaccine is used that is commonly
combined with tetanus and pertussis vaccine
(DPT) and given intramuscular to children
at the age of 2, 4 and 6 months. A booster
dose is given a year later and another at
school age.
B- Passive immunization: Anti-toxin
serum is given to contacts of a case.

21. Bacillus anthracis
Morphology:
Large Gram positive bacilli, arranged in long
chains, non-motile, sporulated in vitro, the spores
are oval, central and not stained with Gram stain.
Pathogenesis (Anthrax):
Anthrax is primarily a disease of farm animals e.g.
cattle and sheep. Man is infected by coming in
contact with diseased animals or their dead bodies.
Farmers, butchers and veterinary doctors are more
liable to get infection. Infection could occur in
different forms, the commonest forms are:
1- Cutaneous anthrax (malignant pustule): The
organism enters through skin abrasions. A necrotic
ulcer is formed.
2- Pulmonary anthrax (wool sorters disease): It
results from inhalation of spores leading to

22. Diagnosis:
1- Specimen: exudates of malignant pustule
vesicle, sputum or stool.
2- Gram stained smear.
3- Culture: on nutrient agar or blood agar at 37 C
for 24 hours.

23. Genus Clostridium
The Clostridia are anaerobic spore forming
Gram-positive bacilli. Most of them are motile and
non-capsulated.
C. tetani: The causative agent of Tetanus:
- C. tetani are long Gram positive bacilli arranged
singly or in chains, motile, spore forming, the
spores are terminal and spherical giving the
characteristic drum stick appearance.
- Tetanus is a type of wound infection
characterized by release of neurotoxin that causes
generalized muscle spasm.
o C. perfringens: The causative agent of Gas
gangrene.
- A type of wound infection,
- Characterized by muscle necrosis, bad odor and

24. • C. botulinum: The causative agent of
Botulism.
- A type of food poisoning, specially canned food.
- Caused by release of powerful exotoxins.
- Causes flaccid muscle paralysis.
• C. difficile: The causative agent of
Pseudomembranous colitis.
- C. difficile is one of the normal flora in the GIT
of man, this organism can't compete with normal
intestinal flora but with prolonged use of
antibiotics especially in elderly or immune-
compromised individuals, the antibiotics eliminate
the normal flora, Cl. Difficile can flourish,
producing disease

25. Acid fast bacilli
MYCOBACTERIA
Mycobacteria are obligate aerobe, non-motile,
non-spore forming bacilli.
Mycobacteria are not classified as either Gram-
positive or Gram-negative.
Difficult to stain due to high lipid content of the
cell wall, once stained, they resist decolourization
with acids and that is why they are described as
“acid fast bacilli ".
Mycobacterium tuberculosis
Morphology:
Small, straight or slightly curved bacilli, non-
motile, non-sporulated, occur singly, in pairs or in
masses. Not stained by Gram but can be stained by
Ziehl - Neelsen (Z.N.) stain. Once stained they
resist decolourization with acid and alcohol (i.e. Acid
and alcohol fast).

26. Cultural characters:
Obligate aerobe.
Optimum temperature is 37 C.
Very slow grower, may require 4 - 6 weeks to get
visual colonies.
Cannot grow on ordinary media it requires an
enriched egg based media called Lowenstein-Jensen
(L.J.).
Pathogenicity:
M. tuberculosis is the etiologic agent of
tuberculosis (T.B.) in humans.
Tubercule bacilli enter the alveoli by airborne
transmission.
They resist destruction by alveolar macrophages,
forming the primary lesion.
They spread to regional lymph nodes and enter
the circulation

27. Diagnosis of pulmonary tuberculosis:
1. Clinical specimens: sputum, bronchial or
gastric washings.
2. Direct smear:
Stained by Ziehl-Neelsen stain.
Acid-fast bacilli appear pink in a contrasting blue
background.
3. Culture:
Inoculated on Lowenstein-Jensen media.
All cultures should be examined weekly for 4-8
weeks.
4. Intradermal skin test (Tuberculin):
Definition: It is a skin allergic test, used to detect
immunity to tuberculosis which becomes

28. Prevention and control:
1. General measures
• Early case finding and effective treatment.
• Applying proper infection control measures in
hospitals.
• Avoid overcrowding.
• Pasteurization of milk.
2. BCG vaccine:
The vaccine used for immunization against
tuberculosis is called B.C.G (Bacille Calmette
Guerin) vaccine. This is a living attenuated vaccine.
The aim of B.C.G vaccination is to produce a
minimal controlled tuberculous focus which creates
allergy and immunity that last for 2-5 years. It is
given as a single dose by intradermal injection in
the deltoid region.
B.C.G vaccination is given to children during the
first year of life. It is also given to high risk adults

29. GRAM NEGATIVE BACILLI
1) ESCHERICHIA COLI (E. Coli)
Morphology: Gram negative bacilli, motile,
non-spore forming and some strains are
capsulated.
Pathogenicity:
E. coli is the most common cause of urinary
tract infections.
Diarrheal diseases.
Neonatal meningitis.
It is an important cause of hospital acquired
infections, wound sepsis, appendicitis, peritonitis,
cholecystitis, otitis media .........etc.

30. 2) Klebsiella:
Morphology: Gram negative bacilli, non-
motile, non-spore forming and capsulated
both in tissue and in vitro culture.
The main species of medical importance are:
1. Klebsiella aerogenes: It is a frequent cause
of urinary tract infection.
2. Klebsiella pneumonia (Friedlander’s
bacillus):
- It causes a sever form of lobar pneumonia
with a relatively high mortality.
- It also causes urinary tract infection.

31. B.R.: Coliform bacilli ferment all sugars with acid
and gas
The main Biochemical differences between them can
be tabulated as follows:
Orgamism ( I ) ( M ) ( V ) ( C )
E. Coli + + _ _
Klebsiella _ _ + +
Citrobacter _ + _ +
(I) indole (m) methyl red (v) vogus preskaur
(c) citrate

32. B) Lactose non fermenters
1) Salmonella
The main species of medical importance are:
1- Salmonella causing enteric fever:
- Salmonella typhi. - S. paratyphi A.
- S. paratyphi B. - S. paratyphi C.
2- Salmonella causing food poisoning:
- S. typhimurium. - S. enteritidis.
Morphology:
Gram negative bacilli, motile, non-spore forming
and may be capsulated.
Cultural characters:
- Aerobic and facultative anaerobes.
- Optimum temp. 37 C
- Grow on MacConKey’s agar medium producing
pale yellow colonies being non lactose fermenters

33. Pathogenicity: Enteric fever
The organisms enter the body by oral route in
contaminated food or drinks. Once the
organisms enter the intestine, they multiply in
peyer’s patches and then pass through the
lymphatics to the blood stream causing
bacteremia that persists for one week .Then
they disseminate to the liver to be excreted
through bile into the intestine and to the kidney
where it be excreted in urine.
Diagnosis of enteric fever:
There are two main lines: direct and indirect
methods. The choice of the method depends on
the stage of the disease

34. 1- DIRECT METHODS:
a) Isolation from blood (blood culture):
In the first week of the disease. This is done by adding
5-10 ml of patient’s blood to 50-100 ml broth. After 24
hours incubation at 37 C subculture is made on
MacConkey’s medium. Any pale yellow (non lactose
fermenting) colonies are picked and further identified by
morphology, biochemical characters and serologic typing
by slide agglutination with specific anti-O and anti-H
sera .
b) Isolation from stools (stool culture):
The organism may appear in the stools all throughout
the course of disease, but are most frequent during the
second & third weeks. The stool specimen is put into
an enrichment medium such as selenite or
tetrathionate broth which inhibits multiplication of the
normal intestinal flora and permit multiplication of
salmonella.

35. After incubation at 37 C for 1-2 days, subculture is
made on a selective medium such as SS (Salmonella
Shigella) agar or DCA. The suspected colonies from
these soild media are further identified as before c)
Isolation from urine:
Salmonella usually appear in urine from the second
week onwards. Urine is obtained under complete
aseptic precautions and examined by plating the
centrifuged deposit on Mac-Conkey’s medium. After
24 hours incubation the suspected growth is
identified as before.

36. 2- INDIRECT METHOD:-
(The Widal test)
Definition: It is an agglutination test used
in diagnosis of enteric fever. Agglutinating
antibodies begin to appear in the serum of the
patient during the second week of fever and
reach maximum about the end of the third
week and persist for several months.
The O-antibodies disappear faster than H-
antibodies, so its presence is more indicative of
current or recent infection.

37. Interpretation of Widal test:-
The following points should be taken into consideration
when interpreting the Widal test:
1- The test is positive only by the begining of the second
week onwards. So if the test is done during first week it
gives false negative results.
2- The diagnostic titre depends on the endemicity of the
disease in the area. In Egypt, where the disease is endemic
the diagnostic titre is not less than 1/80 or higher. Low
titres can be found in normal population due to previous
subclinical infection.
3- In suspected cases with a titre below 1/80 a second
serum sample is taken after 7-10 days later and the test is
repeated. If there is a rising titre, this indicates infection.
4- If agglutination occurs with more than one H-antigen
suspension, this means a post vaccination (TAB vaccine)
reaction.
5- If patient received antibiotic therapy early in the disease,
the drug will reduce the antigenic mass and subsequently
the patient’s antibody response will be suppressed. The
antibody titre in such patients will be suppressed.

38. SHIGELLA
Members of this genus are the causative organisms
of bacillary dysentery.
Morphology: Gm -ve bacilli, non- motile, non-
spore forming
Pathogenicity: Bacillary dysentery
The organism enters the body by the oral route in
contaminated food and drinks. The incubation
period is from 12 hours to few days (1-2 days).
There is sudden onset of abdominal pain, diarrhea,
tenesmus and pyrexia. Stool composed mostly of
blood, pus and mucous.
Diagnosis:
a) Specimen: stool.
b) The mucous bloody part of the stool is cultured
on selenite or tetrathionate broth for 12-18 hours
at 37 C then subcultures are made on MacConky’s
or DCA or S.S. agar plates.

39. Pseudomonas aeruginosa
Morphology: Gm -ve rods, motile, non-spore
forming.
B.R.: oxidase positive, ferment no sugar.
Culture characters: Strict aerobic, grow at 37o
C, grow on nutrient agar medium producing soluble
pigments (exopigment).
Diseases caused by Pseudomonas
aeruginosa:
- Skin infection eg. Burn sites, wound and ulcers.
- Respiratory tract infections.
- Urinary tract infections.
- External ear infections and otitis media.
- Eye infections.

40. Proteus
Morphology: Gm -ve bacilli, motile, non-
capsulated, non-spore forming.
B.R.: Urease positive.
Cultural characters:
Proteus is highly motile; on nutrient and blood agar
they produce a characteristic “swarming” growth.
(successive waves of growth).
On MacConkey’s agar, swarming is inhibited and
compact pale (non- lactose fermenting) colonies are
formed.
Diseases caused by Proteus:
- Wound infections. - Otitis media.
- Summer diarrhea in infants. - Urinary tract infections.

41. Vibrio Cholera
Morphology: Comma shape, actively motile,
Gram-negative bacilli.
B.R.: Oxidase test positive.
Cultural characters: Highly aerobic. Can be
isolated on TCBS (selective medium) agar medium
producing yellow colonies.
Pathogenicity: the causative organisms of
Cholera which transmitted orally by contaminated
food or drinks.
Bordetella
Bordetella pertussis is the most important
member of this genus. It causes whooping cough
which is a disease of children. Infection occurs by
respiratory route (by droplets) from early cases and
possibly via carriers.

42. The Brucella group
They are short, Gram negative bacilli which are
essentially pathogens of animals. In man, they
cause brucellosis (Undulant fever or Malta fever).
SPIROCHETES
Spirochetes are slender spiral organisms, they
range from obligate anaerobes to aerobes and
from free living forms to obligate parasites.
Treponema pallidum, the causative agent of
syphilis is a member of this family. It is slender
spiral cannot be stained by Gram stain, stained
by Giemsa and Fontana stain. Live treponemes
can be seen unstained by dark-field microscopy.
It cannot be cultivated.
Syphilis is strictly human disease, transmitted
by sexual contact.

43. Virology
Viruses are the smallest known infective obligate
intracellular agents. They infect most forms of life
(human, animal, plants and bacteria).
►General Properties of viruses:
1. Viruses are the smallest infectious agents known
therefore:
They are seen only by the electron microscope.
They can pass through the bacterial filters.
2. Viruses are a cellular (don't have nucleus, don't
have organelles such as ribosomes, mitochondria
and lysosomes).
3. Viruses contain either RNA or DNA as genome
and never both.
4. They are metabolically inert (they have no
activity outside host cell).
5. They are obligate intracellular parasites (they are

44. Structure of viruses:
1. Viral nucleic acid (genome):
Viruses have one type only of nucleic acid, either DNA or
RNA, accordingly, viruses are classified into either DNA or
RNA viruses
Viral genome may be single stranded (ss) or double stranded
(ds) , linear or circular, intact or segmented.
It is the essential infectious component of the virus
Viral capsid:
Protein coat which surround and enclose viral nucleic acid .
The capsid with its enclosed nucleic acid is called
nucleocapsid.
Functions of viral capsid:
1- It protects the viral nucleic acid.
2- Attachment of virus with susceptible host cell .
3- Viral proteins are antigenic and immunogenic .
3. Viral envelope:
It is a lipoprotein coat acquired by some viruses as they bud
from the host cell during their replication.

45. RNA VIRUSES
1} POLIO Viruses
Pathogenesis:
Polioviruses are the causative agent of poliomyelitis. Infection
is transmitted by ingestion of the virus in faecally contaminated
food or drink as water. Droplet infection can also occur.
The mouth is the portal of viral entry, the virus multiplies in the
oropharynx and the intestine, progress and reach the local
lymph nodes with invasion of the blood stream giving viremia.
The virus then reaches the CNS leading to destruction of the
lower motor neurons and flaccid paralysis. Death may occur
from paralysis of the respiratory muscles. The infection is
followed by long-lasting immunity to the same antigenic type of
the virus.
Laboratory Diagnosis:
1-Virus isolation: the virus can be isolated from throat swabs
or stool.
2-Serology: by detection of antibodies against the virus in
patient serum.

46. Prevention and Control Measures:
I- General Measures:
a) Isolation of patients diagnosed to have
poliomyelitis.
b) Operations as tonsillectomy and injections as
vaccinations must be avoided in children with fever in
endemic area.
c) Proper sewage disposal and safe water supply.

47. Salk vaccine :
It is a formalin - killed vaccine prepared from the 3
virus types.
Given by S.C. injections, in 3 doses and periodic
booster doses are necessary to maintain immunity.
Advantage :
1- Induces systemic immunity.
2- Can be given to immune- deficient or immune-
suppressed persons.
3- Can be given to pregnant mothers.
Disadvantage :
No intestinal (local) immunity.
Sabin vaccine
It is a live attenuated vaccine Prepared from non-
paralytic mutants of the three antigenic types of
polioviruses.

48. Given orally to infants at 2, 4, 6 & 18 months of age.
A booster dose is recommended for all children at the
age of school entry.
Advantage :
1. It is given orally so it is easier to be taken and large
number of persons can be immunized in a short time.
2. Stimulate immunity similar to that of natural
infection i.e. produce both local & systemic immunity.
3. It leads to mass vaccination.
Disadvantage
1. If the alimentary tract of a child is infected with
another virus at the time the vaccine is given, the
development of immunity may be blocked. 2. Its
potency decreases if kept unfrozen.
3. Any gastrointestinal troubles will interfere with the
vaccine absorption.

49. Mumps Virus
Pathogenesis:
The virus is transmitted by droplet inhalation or
by the oral route, leading to fever, swelling of one
or both parotid and submaxillary glands. Meningo-
encephalitis, orchitis, oophoritis and infertility may
complicate some cases. An attack is followed by
long -lasting immunity.
► Prophylaxis:
Mumps live attenuated vaccine is available in
combination with measles and rubella vaccines
(MMR), all in the live attenuated form. It is given
S.C. in one single dose after 9 m of age up to 15
m of age to avoid failure of vaccination which
results from the presence of residual maternal
antibodies.

50. Measles virus
Pathogenesis:
Infection occurs by droplet inhalation. The disease is
characterized by high fever and skin rash. The disease
may be complicated with otitis media, pneumonia or
encephalitis. One attack of measles is followed by life-
long immunity.
► Prophylaxis: MMR vaccine.
Rubella virus
► Pathogenesis:
The disease is transmitted by droplet infection and
is manifested by mild fever with skin rash. Rubella
infection leads to congenital defects in the fetus that
may be in the form of deafness, cardiac abnormalities,
cataract and mental retardation. Infection with rubella
is followed by life - long immunity.
► Prophylaxis: MMR vaccine

51. Human Immune Deficiency Viruses (HIV)
The virus is the leading cause of AIDS (Acquired
immunodeficiency syndrome). There are two types of
HIV which are HIV 1 and HIV 2.
The Virus present in all body fluids.
Mode of infection:
1- Sexual intercourse. 2- Blood transfusion.
3- Contaminated syringe. 4- Renal dialysis.
5- Congenital, during birth, breast feeding.
High risk group:
1- Medical and paramedical staff. 2- Drug addict. 3-
Homosexual.
Pathogenesis:
The virus binds T helper cells leads to destruction
and dysfunction of T helper cells that result in
decreasing Cell-mediated immunity with increase
incidence of opportunistic infection and tumors which
ends by patient death.

52. Prophylaxis:
I- General measures:
1. Good screening of blood before transfusion.
2. Use of disposable sterile single use syringe.
3. Strict sterilization of surgical instruments.
4. Safe sex.
5. Adhering to religion.
6. Health awareness.
II- Immunization:
There is no specific vaccine against HIV till now
but only trials.

53. DNA viruses
Herpesviruses
a} Herpes simplex viruses (HSV)
- Types: There are 2 herpes simplex viruses, type 1 and type
2.
- Transmission and pathogenesis:
HSV-1 is transmitted primarily in saliva→ mainly orofacial
lesions.
HSV-2 is transmitted by sexual contact → Genital lesions.
Reactivation
Latency
Primary infection
Reactivation in
response to
various stress
stimuli as common
colds, sun light.
Herpes libialis:
vesicles, crust at
lips or nose.
- HSV-1 in
trigeminal ganglia.
- HSV-2 in sacral
ganglia.
HSV-1:
- Acute
gingivostomatitis.
Keratoconjunctiviti.
- Encephalitis.
- Disseminated
infections.

54. HSV-2:
- Genital herpes: vesicles on the external genitalia
as well as the cervix
- Neonatal infection: contact between fetus &
vesicular lesions within the birth canal generalized
disease.
Varicella-Zoster virus (VZV)
- The same virus causes both varicella (primary
disease) & zoster (recurrent form).
a- Primary infection: Chicken pox
Fever + characteristic vesicular rash on the
trunk, limbs and face.
b- Latency.
c- Reactivation: Zoster or shingles
Prevention: VZV vaccine: a live attenuated vaccine

55. Hepatitis viruses
1. Hepatitis A Virus (HAV)
- Transmission: food born.
- Clinical Features:
Mild disease.
Fever, jaundice are main symptoms.
99% cases recover completely.
- Laboratory diagnosis:
Detection of HAV-specific IgM in the patient's
blood.
- Prevention and treatment:
Assurance (no specific treatment).
Currently, two Hepatitis A vaccines are available.
A combined hepatitis A and B vaccine.

56. 3. HCV
2. HBV
RNA
DNA
Type of virus
Parenteral
Parenteral
During birth
Breast milk
Sexually
Transmission
+
+
Hepatoma
Insidious
Insidious
Onset
Elevated 1-6
months or
more
Elevated 1-6
months or
more
Liver enzymes
Bad
Bad
Prognosis
1
%
Less than 1%
Mortality

57. Diagnosis of hepatitis B & C:
I) HBV:
PCR: detect virus nucleic acid in sample.
* Hepatitis markers:
o HBsAg: diagnose HBV infection.
o HBsAb: Indicate recovery.
o HBcAg: not detected in blood (in liver only).
o HBcAb:
IgM → diagnose recent HBV infection.
IgG : → past exposure or infection.
o HBeAg: Indicates active viral replication.
o HBcAb: Less viral infectivity .
II) HCV:
HCV Ab: diagnose HCV infection.
Quantitive PCR: done before and after treatment

58. Prophylaxis:
a- General lines:
1. Good screening of blood before transfusion.
2. Use of disposable sterile single use syringe.
3. Strict sterilization of surgical instruments.
4. Safe sex.
5. Adhering to religion.
6. Health awareness.
b- Specific: HBsAg vaccine:
Recombinant DNA vaccine.
indicated in :
a- Doctors and nurses.
b- Patients with frequent blood transfusion.
c- Sexual partner of chronic HBV.
d- Infant born to HBV carrier mothers.
e- Universal immunization of infant.

59. Applied Microbiology
MENINGITIS
Septic meningitis:
The three most important pathogens are:
1- Neisseria meningitides
2- Streptococcus pneumoniae
3- Haemophilus influenzae (type b).
II) Aseptic meningitis:
Polioviruses * Herpes viruses (Herpes simplex
virus, VZV).
* Mumps virus. * Measles virus.
III) Tuberculous meningitis.
IV) Fungal causes of meningitis.:
Cryptococcus , candida ,
aspregillus,histoplasma

60. RESPIRATORY TRACT INFECTIONS
I) Infection of throat and pharynx (sore
throat and pharyngitis):-
The most common organisms involved are:
a) Bacteria: Streptococcus pyogenes and
Corynebacterium diphtheriae.
b) Fungi: Candida.
c) Virus: e.g. Herpes viruses.
II) Infection of the ear and sinuses:
Causative organsims:
a) Bacteria
- Haemophilus influenze. - Streptococcus
pyogenes.
- Sterptococcus pneumonia. - Staph aureus.
- Pseudomonas and Proteus - Coliform bacilli
b) Fungi: e.g. candida. A fungal infection of the
ear is called otomycosis.

61. III) Infection of the lungs (pneumonia):
Causative organisms:
a) Bacteria:
1- Strept. pneumoniae is the commonest cause of
lobar pneumonia and bronchopneumonia in young
children and elderly.
2- Haemophilus influenzae
3- Staph. aureus
4- Strept. pyogenes
5- klebsiella pneumoniae
6- E.Coli, Proteus and Pseudomonas
7- Mycobacterium tuberculosis
b) Viruses: e.g. - Influenza A virus - Measles
c) Fungi.

62. BACTERIAL FOOD POISONING
Types and causative organisms:
A- Toxic types:
Staphylaococcus food poisoning.
Clostridium botulism.
Bacillus cereus food poisoning
B- Infective types:
Salmonella food poisoning; S. typhimurium
& S. enteritidis
C- Infective toxic e.g. Cl. Welchii.

63. URINARY TRACT INFECTION
Causative organisms:
- E. coli causes 60-90% of urinary infections.
- Staph epidermidis, Staph aureus and Staph saprophy
- Klebsiella , Proteus or Pseudomonas
- Mycobaterium tuberculosis.
- Fungi as Candida albicans.

64. DISEASES TRANSMITTED FROM
MOTHER TO FAETUS OR NEWBORN
1] Congenital infections {In Utero}
(TORSH)
Important causes of congenital infections:
• Toxoplasmosis
• Rubella virus.
• syphillis
• Hepatitis B virus , HIV , HSV
• Others (vzv ,cytomegalo virus ).
2] Neonatal infections: Acquired during
passage down in an infected birth canal.
e.g: - Neisseria gonorrhoeae --> ophthalmia
neonatorm.
- Herpes simplex virus.

65. GOOD LUCK