Microaspiration from nasopharynx: S. Pneumonia Inhalation: TB, viruses, Legionella Aspiration: anaerobes Bloodborne: Staph endocarditis, septic emboli Direct extension: trauma Microaspiration from nasopharynx: S. Pneumonia Inhalation: TB, viruses, Legionella Aspiration: anaerobes Bloodborne: Staph endocarditis, septic emboli Direct extension: trauma Microaspiration from nasopharynx: S. Pneumonia Inhalation: TB, viruses, Legionella Aspiration: anaerobes Bloodborne: Staph endocarditis, septic emboli Direct extension: trauma Microaspiration from nasopharynx: S. Pneumonia Inhalation: TB, viruses, Legionella Aspiration: anaerobes Bloodborne: Staph endocarditis, septic emboli Direct extension: trauma Microaspiration from nasopharynx: S. Pneumonia Inhalation: TB, viruses, Legionella Aspiration: anaerobes Bloodborne: Staph endocarditis, septic emboli Direct extension: trauma CAP usually caused by a single organism Even with extensive diagnostic testing, most investigators cannot identify a specific etiology for CAP in ≥ 50% of patients. Caused by a variety of Bacteria, Viruses, Fungi Streptococcus pneumoniae is the most common pathogen 60-70% of the time

1. Introduction
to
Microbiology
Medical Microbiology & Immunology

2. MICROBIOLOGY ??
Bacteri
a
Viruse
s
Fungi
Protozoa
&
Helminth
s
Micro: very small
(needs a
microscope to be
seen).
Biology: is the
study of living
organisms.
Microbiology: The
science that study
the
microorganisms
that cannot be seen
without the use of a
microscope.
Definitions

3. Classification of microorganisms
Acellular
 They are not cells.
 No cell membrane.
 It is a nucleic acid
protected by a protein
coat.
 They can live and
reproduce only inside a
living cell.
 ex. Viruses
Cellular
Prokaryotes Eukaryotes
 Have no nucleus.
 Have no
membrane bound
organelles
 ex. Bacteria,
Archaea
 Have true nucleus.
 Many membrane
bound organelles.
ex. Protozoa,
Fungi,
Helminths.

4. Prokaryotes Eukaryotes
Nuclear
membrane,
nucleus & nucleoli
No Yes
Membrane bound
organelles
No Yes
Mitochondria, Golgi ap., ER
Number of
chromosomes
One chromosome
without histones
Multiple chromosomes with
histones.
Energy production By the cell
membrane.
By mitochondria.
Ribosome 70s ribosome
(50s & 30s)
80s ribosome (60s & 40s)
Cell wall Peptidoglycan Polysaccharide (if present)
Multiplication Simple binary fission Mitosis & meiosis
Examples  Bacteria  Fungi
 Protozoa
 Helminths

6. Classification of Bacteria
Bacteria are classified according to their:
1. Morphology (shape & arrangement)
2. Staining reaction (Gram stain, Acid fast
stain)
3. Cell wall
1- Bacteria

7. 1- Morphological classification (Shape & arrangement):
A)Cocci: Spherical or oval cells.
- Pairs: diplococci: as Streptococcus pneumonia, Neisseria
species.
- Chains: as Streptococcus pyogenes.
- Grape like clusters: Staphylococci as Staphylococcus
aureus.

8. Cocci bacteria

9. B) Bacilli: Rod shaped bacteria
- Chinese letters
- Coccobacilli
- Comma shaped (Vibrio)
- Club shaped

10. C) Spirochetes: Long slender, spiral
shaped with several coils

11. 2- According to staining reaction:
Gram stain:
Gram positive:
• Cocci: Staphylococcus, Streptococcus
• Bacilli: Bacillus, Clostridium.
• Gram negative:
• Cocci: Neisseria, Moraxella.
• Bacilli:
• Enteric rods: Escherichia coli , Klebsiella,
Salmonella, Shigella, Vibrio, Brucella, and
Pseudomonas.
• Non-enteric rods: Haemophilus.

12. Gram positive cocci Gram negative
cocci

13. Gram positive Bacilli Gram negative bacilli

14. Acid Fast stain (Ziehl-Neelsen stain):
Acid fast bacilli: Mycobacterium tuberculosis

15. 3- According to the cell wall:
Three groups:
1. Lacking Cell Wall: Mycoplasma.
2. Flexible Cell Wall: Spirochetes e.g.
Treponema.
3. Rigid Cell Wall:
A. Filamentous bacteria: e.g.
Streptomyces (antibiotic producers).
B. Simple Unicellular:
o Obligate intracellular bacteria: e.g.
Rickettsia, Chlamydia.
o Free-living bacteria:

16. Medically Important Bacteria
Lacking
cell wall
Rigid cell
wall
Filamentous
Simple
unicellular
Obligate
intracellular
parasite
Free living
Gram positive
Rods
(bacilli)
Cocci
Gram
negative
Rods
(bacilli)
Cocci
Flexible
cell wall
Aerobic and
anaerobic

17. Type of bacteria
A. Pathogenic bacteria:
- Cause disease in humans:
Example Salmonella typhi (cause typhoid fever
or enteric fever).
B. Commensal bacteria (normal flora) (Human
microbiome):
 Normally inhabit the human body.
 Mostly bacteria but may be fungi as Candida.
 Do not cause disease in immuno-competent humans.

18. o Skin:
Staphylococcus epidermidis (90%) & Staphylococcus aureus.
Propionibacterium acnes reside in hair follicles and sebaceous glands.
o Nose:
The same skin normal flora.
o Eye:
The same skin normal flora + Moraxella.
oMouth:
The same skin normal flora + Streptococcus mutans , Lactobacillus &
Candida spp.
o Intestinal tract:
Mostly anaerobes (e.g. Bacteroides, Clostridium), E. coli, Klebsiella,
Enterococcus faecalis, & Candida.
o Female Genital tract: Lactobacillus & Candida albicans.
Distribution of Normal Flora in the Body

19. Beneficial Role of Normal Flora
1. Compete for nutrients and attachment sites.
2. Produce antimicrobial substances.
3. Bacterial colonization of a newborn acts as a
powerful stimulus for the development of the
immune system.
4. Gut bacteria provide important nutrients, such as
vitamin K, and aid in digestion and absorption of
nutrients.
5. Lactobacilli in the vagina keep acidic pH of the
vagina.

20. Cause infections in the following conditions:
 Displacement from their normal site in the body to an
abnormal site (e.g. S. epidermidis, into the bloodstream
where it can colonize catheters and artificial joints).
 Depletion of the numbers of flora (e.g. antibiotics
overuse leads to:
1) Overgrowth of antibiotic-resistant Clostridium difficile in colon
, causing severe pseudomembranous colitis in children.
2) Depletion of Lactobacilli in vagina and overgrowth of
Candida.
 Intestine commensal bacteria might convert the ingested food into
carcinogenic derivatives.
 When individuals are immunocompromised, the normal flora can
overgrow and become pathogenic (opportunistic infections).
Harmful Effects of Normal Flora

21. Pathogenicity of microorganisms
Source of Infection
• The environment: soil, air & water.
• Animals: zoonotic diseases.
• Humans:
A. Case: patient.
B. Carrier: person carrying the pathogen
without having the disease→ dangerous
source of infection as not known to others.

22. Mode of Transmission= Routes of Infection
1. Contact:
Direct: hand to hand, body secretions, Sexual as HIV, HCV, HBV,
Neisseria gonorrhea & Treponema pallidium.
Indirect: through contaminated surfaces or objects.
2. Airborne: Tuberculosis, Measles, Chickenpox.
3. Droplet: Neisseria meningitides, influenza virus & COVID-19.
4. Ingestion: fecal-oral: Salmonella enteric fever and poliovirus
infection.
5. Bloodborne: HIV, HCV & HBV.
6. Arthropod-borne (by insects): ArBo viruses, Malaria.
7. From mother to fetus:
Tran placental transmission: e.g. Rubella, Cytomegalovirus, &
HIV (congenital infections).
Vertical: (through birth canal) e.g. Treponema pallidium, HBV,
HCV & HIV.

23. One month after starting amoxicillin for sinusitis, a-4-year-
old girl is brought to the emergency department with fever
and diarrhea. She has been diagnosed as
pseudomembranous colitis. Her antibiotic therapy was
discontinued. Which of the following is the most likely
underlying cause for her case?
Case study
A. Development of Allergic reaction
B. Presence of gastric ulcer
C. Mechanical blockage of the large intestine
D. Overgrowth of pathogenic Clostridium difficle

24. Reference
•Lippincott Illustrated Microbiology 4th
edition, Chapters: 1 & 2