lecture notes

1. Introduction to Microbiology
NMB 240
NMB 340
MPM 260

2. “You never truly understand something until
you can explain it to your grandmother”
-- Albert Einstein

3. Understanding of the pathogenesis of virulent organisms, their
epidemiology, host defense, and treatment strategies is an
important aspect of medical microbiology.
Microbiology
Microbiology has utmost relevance in health care units, and it is
important for health care professionals to understand the
pathogenesis and control of infectious diseases.
The mode of action of various antibiotics, the concept of antibiotic
resistance, and multi-drug resistance are important apart from the
methods of vaccination, types of vaccines, and schedules involved in
vaccination.
The role of the normal flora as opportunistic pathogens is critical

4. Objectives
1. Define microbiology
2. List the types of microorganisms
3. Describe the division of microbiology
4. Explain the environment, agriculture, industrial and health
application of microbiology
5. Appreciate the development of early microbiology
6. Appreciate the golden age of microbiology
7. Explain the germ theory of disease
8. Explain the theory of spontaneous generation & biogenesis
9. List Koch’s postulates of disease
10.Understand the importance of microbiology in clinical
practice

5. •Microbiology:
• Microbiology is the specialized science that deals
with the study of organisms that require
magnification to be observed (>.1mm)
•Employs techniques:
• sterilization and the use of culture media –
necessary for isolation and growth of
microorganisms.
Introduction

6. • What are microorganisms?
• Generally smaller than the human eye can detect and belong
to each of the five kingdoms: Monera, Protista, Fungi,
Plantae, and Animalia.
• The subjects of microbiology include bacteria, algae, fungi,
protozoa, and helminths all of which are cells and viruses
which are not cells.
• The majority of microbes exist as single cells or clusters of
single cells; however some are multi-cellular existing as
filamentous multi cells.
• Microorganisms or Microbes:
• Oldest organisms evolved over 3.5 – 3.8 billion years ago

7. •Microorganisms are ubiquitous:
• EveryWHERE
• From deep in the earth’s crust-- to the polar ice
caps and oceans -- to the bodies of plants and
animals.
• Mouth, colon, ears, teeth, arms, hands, feet,
feces, skin, vagina, external eye, upper respiratory
tract, just to name a few places…

8. Definitions
A. Micro/bio/logy –
• Micro_ small; bio_ living; logy_ Study
• study of microscopic organisms, organisms that are invisible to the
naked eye.
B. Microorganisms included :
1. Bacteria - simple, single cell
2. Fungi - single & multi cell forms - yeast, filamentous molds,
complex fungi
3. Protists - single cell, some multicellular - algae, protozoans,
slime molds
4. Viruses - acellular, intracellular parasites
5. Helminths (Worms) - multicellular, more complex

9. Divisions of Microbiology
Organisms studied
1. Bacteriology – study of bacteria
2. Mycology – study of fungi
3. Phycology - study of algae
4. Protozoology – study of protozoa
5. Virology - study of viruses
6. Parasitology – study of parasites

10. Divisions of Microbiology (cont’d)
Health related
1. Etiology – identification of causative agent of disease
2. Epidemiology – study of spread of disease
3. Immunology – study of immune system
4. Chemotherapy – treatment of disease with chemical compounds
5. Infection control – control of spread of infectious disease

11. Divisions of Microbiology (cont’d)
Processes, Functions
1. Microbial metabolism - obtains the energy and nutrients for
survival
2. Microbial genetics - transmission of hereditary characters
3. Microbial ecology - relationship with one another and with their
environment

12. Why Study Microbiology?
Beneficial Applications
1. Impact on Human Health
A. Causative agents of infectious diseases
B. Normal flora
1. Beneficial metabolic functions
2. Antagonistic effect - prevents invasion of pathogens,
over growth of potential pathogens
3. Normal flora vs. identification of pathogen

13. Why Study Microbiology?
Beneficial Applications
2. Environmental importance
A. provide safe drinking water;
B. development of biodegradable products - decomposers
C. use bacteria to clean up oil spills, etc. – called
bioremediation.
D. Food chain
E. Sewage treatment

14. Why Study Microbiology?
Beneficial Applications (cont’d)
3.Industrial importance
A. Food industry (beer, wine, cheese, bread),
B. Brewing industry
C. Pharmaceutical industry (antibiotics, insulin)
D. Genetic engineering

15. Why Study Microbiology?
Beneficial Applications (cont’d)
4. Research importance
A. Agriculture research has led to healthier livestock and
disease-free crops.
B. Research - genetics, metabolism
A. Simple cell structure
B. Rapid rate of growth
C. Inexpensive to culture

16. Microbiology History
“You have to know the past to understand the present.”
― Carl Sagan

17. Microbiology History
• Ancestors of bacteria
were the first life on
Earth
• 1665: Cell theory –
Robert Hooke
Development of Early Microbiology
 1673: First
microbes observed –
Anton van
Leeuwenhoek

18. Development of Early Microbiology
• Anton van Leeuwenhoek (1673)
A. First person to use microscopes to observe microbes
B. Used simple instrument (handheld microscope) to
examine stagnant H2O, etc.
C. Observed microscopic organisms - called them
“animalcules”
D. Submitted detailed descriptions and drawings to the
Royal Society of London
E. Question raised - where did they originate from ?

19. From his teeth, he observed
(A) & (B)- rod forms
(C) & (D)- motion pathway
(E)- Spherical form
(F)- Longer type of spherical form
(H)- Cluster
-Royal Society letter (Sept 17th, 1683)
•Anton van Leeuwenhoek
animalcules

20. Spontaneous Generation & Biogenesis
• Spontaneous Generation – shaped the science of
microbiology:
• Spontaneous Generation refers to the ancient belief that living
organisms could arise spontaneously from nonliving matter.
• The Greek philosopher Aristotle believed insects and other small
animals had to arise by spontaneous generation because he was
unable to observe organs (including reproductive organs).
• Abiogenesis and Biogenesis:
• Abiogenesis: Spontaneous generation
• Biogenesis: Living things only arise from other living things

21. Debate over
Spontaneous Generation & Biogenesis
•Aristotles’s doctrine of spontaneous generation.
Hypothesis that living organisms arise from non-
living matter; a “vital force” forms life
•Biogenesis: Hypothesis that the living organisms
arise from pre-existing life

22. Conditions Results
Three jars covered with
fine net
No maggots
Three open jars Maggots appeared
From where did the maggots come from?
What was the purpose of the sealed jars?
Spontaneous generation or biogenesis?
1668:Francesco Redi
• the beginnings of experimental science
• filled 6 jars with decaying meat

23. Conditions Results
Nutrient broth heated,
then placed in sealed flask
Microbial growth
From where did the microbes come from?
Spontaneous generation or biogenesis?
1745: John Needham
• Objections
• Put boiled nutrient broth into covered
flasks

24. Conditions Results
Nutrient broth placed in
flask, heated, then sealed
No microbial growth
Spontaneous generation or biogenesis?
1765: Lazzaro Spallanzani
• boiled nutrient solutions in flasks

25. Conditions Results
Nutrient broth placed in
flask, heated, not sealed
Microbial growth
Nutrient broth placed in
flask, heated, then sealed
No microbial growth
Spontaneous generation or biogenesis?
1861: Louis Pasteur
• demonstrated that microorganisms are
present in the air

26. Louis Pasteur (1861) _ Confirmation of Biogenesis
A. Performed experiments to disprove Theory of SG.
a) Filtered air through cotton plug. Placed plug in infusion
broth, broth became cloudy - organisms present in the air.
b) Placed boiled infusion broths in “swan-necked” flasks
c) Flasks remained sterile unless tilted or neck broken.

28. The Golden Age of Microbiology
• The Scientific Method
• Debate over spontaneous generation led in part to development of
scientific method
• A group of observations lead the scientist to ask questions about
some phenomenon
• The scientist generates hypothesis (potential answer to question)
• The scientist designs and conducts experiment to test hypothesis
• Based on observed results of experiment, scientist either accepts,
rejects, or modifies hypothesis

29. The Golden Age of Microbiology

30. The Golden Age of Microbiology(1857-
1914)
Microbiology established
as a science
Louis Pasteur
Spontaneous generation disproved
Wine fermentation (yeasts and
bacteria)
Pasteurization

31. Pre-Pasteur:
• Ignaz Semmelweis (1840s) –
hand disinfection and puerperal
fever(childbed fever)
Based on Pateur’s
and Semmelweis’
findings: Joseph
Lister (1860s) –
antiseptic
surgery (phenol)

32. Pre-Pasteur:
• In 1843, an American physician, Oliver Wendall Holmes
published a paper on Puerperal (PURE-PER-AL) sepsis which
afflicted mothers during childbirth.
• Holmes reported that it was much safer to deliver a baby at
home than in a hospital... where physician-handling
contribute to the disease.

33. 1848, Ignaz Semmelweiss:
• A Hungarian physician on the obstetric ward of a teaching hospital in
Vienna
• Ridiculed for insisting that physicians wash their hands before working
with pregnant women.
• The residents frequently handled cadavers in the morgue before
coming to the maternity ward and he hypothesized that these cadaver
particles were carried from their autopsy studies into the delivery
room and these particles resulted in puerperal fever/ infections.
• Semmelweiss conducted experiments that hand washing would reduce
the incidence of disease from 30% to less than 3%.
• Physicians still refused to wash their hands and admit that they were
unclean

34. Florence Nightingale:
• Born in 1820 to a wealthy British family
• She combined her intelligence and sense of humanity and began nursing in 1845.
• In England, she became well known for her skills as well as her push for
healthcare reform.
• In 1854, she and 40 health practitioners picked by her went to
assist the military hospitals in Scrutari during the Crimean war.
• This was in response to public outcry at the high mortality rates being
reported from frontline reporters, contrary to official military
releases. Within two months of her arrival mortality rates in the
barracks dropped from 42% to 2%.
• This was mostly due to her practice of rigorous sanitation and
infection control.
• Known for introducing cleanliness and other antiseptic techniques into
nursing.

35. Robert Koch
• Work on anthrax proves the
germ theory of disease
• Procedures become Koch's
postulates
• Development of pure culture
technique
Nobel Prize in 1905
Nobelprize.org

36. The Germ Theory of Disease (Robert Koch in the late 1870's)
A. Microbes (germs) cause disease and specific microbes cause
specific diseases.
B. He studied anthrax - disease of cattle/sheep; also in humans
C. He observed that the same microbes were present in all blood
samples of infected animals. He isolated and cultivated these
microbes (now known to be Bacillus anthracis ). He then
injected a healthy animal with the cultured bacteria & that
animal became infected with anthrax & its blood sample showed
the same microbes as the originally infected animals.
D. His experiments proved that particular microbes cause
particular diseases

37. Koch's Postulates:
Four criteria designed to establish a causal relationship
between a causative microbe and a disease. Koch (in
1890) postulated that:
1. The causative agent must be present in every
individual with the disease.
2. The causative agent must be isolated & grown in pure
culture (he invented pure cultures with Frau Hesse's
help, who developed the agar plate method).
3. The pure culture must cause the disease when
inoculated into an experimental animal.
4. The causative agent must be re-isolated from the
experimental animal & re-identified in pure culture.

38. Before the Golden Age Period: The Birth of
Vaccination
• Edward Jenner and
smallpox vaccination
(1796)
 ~ 100 years later: Pasteur shows
how vaccinations work. (Creation of
avirulent strains of bacteria during
extended laboratory cultivation)
Cultured cholera bacterium
and went on vacation

39. The Birth of Modern Chemotherapy
• 1910: Paul Ehrlich developed a synthetic
arsenic drug, salvarsan, to treat syphilis
• 1930s: Synthesis of sulfonamides
• 1928: Alexander Fleming
and the discovery of the
first antibiotic
Fig 1.5

40. Penicillin purification and clinical trials not until 1940s

41. • Martinus Beijerinck (1884 - 85)
• Considered on the founders of virology and
environmental microbiology
• Discovered filterable agents called “viruses”
(toxins, poisons).
• Infectious agents in tobacco plant fluids
• Assumed soluble toxin in filtrate caused
disease
• Called “viruses” (Latin for toxins, poisons)
• Later discovered to be Tobacco mosaic virus

42. Modern Developments in Microbiology
•Bacteriology – Mycology – Parasitology – Virology –
Immunology
•Microbial genetics and molecular biology lead to
Recombinant DNA Technology (genetic
engineering).
• Prokaryotic model system: E. coli

43. Selected Nobel Prizes for Microbiology Research
• 1901 von Behring Diphtheria antitoxin
• 1902 Ross Malaria transmission
• 1905 Koch TB bacterium
• 1908 Metchnikoff Phagocytes
• 1945 Fleming, Chain, Florey Penicillin
• 1952 Waksman Streptomycin
• 1969 Delbrück, Hershey, Luria Viral replication
• 1987 Tonegawa Antibody genetics
• 1997 Prusiner Prions
• 2005 Marshall & Warren H. pylori & ulcers

44. Microbes and Human Disease
– Again many Challenges –
• Normal microbiota (flora) in and on the human body
• Pathogens overcome the host’s resistance infectious disease
• Antimicrobial resistance
• Bioterrorism
• (Re-)emerging infectious diseases (EID): West Nile Encephalitis,
avian influenza, SARS-Severe acute respiratory syndrome, Bovine
Spongiform Encephalopathy, HIV/AIDS . . .

45. • Influenza A virus (H5N1)
• Primarily in waterfowl and poultry
• Sustained human-to-human transmission has not occurred yet
WestNileEncephalitis
 West Nile Encephalitis
• Caused by West Nile virus transmitted by a mosquito
• First diagnosed in the West Nile region of Uganda in
1937
• Appeared in New York City in 1999
What about the Covid-19?

46. MRSA
• Methicillin-resistant Staphylococcus aureus
• 1950s: Penicillin resistance developed
• 1980s: Methicillin resistance
• 1990s: MRSA resistance to vancomycin reported
• VISA: Vancomycin-intermediate-resistant S. aureus
• VRSA: Vancomycin-resistant S. aureus
BovineSpongiformEncephalopathy
Bovine Spongiform Encephalopathy
 Caused by a prion
 Also causes Creutzfeldt-Jakob disease (CJD). New variant
CJD in humans is related to beef consumption

47. Figure 25.12
Escherichia coli O157:H7
• Toxin-producing strain of E. coli
• First seen in 1982
• Leading cause of diarrhea worldwide

48. Acquired immunodeficiency syndrome (AIDS)
• HIV/AIDS
- Caused by human immunodeficiency virus (HIV)
- First identified in 1981
- Worldwide epidemic infecting 30 million people; 14,000 new
infections every day
- Sexually transmitted infection affecting males and females
- HIV/AIDS in the U.S.: 30% are female, and 75% are African
American

49. • Medical microbiology_ the study of the pathogenic microbes and
the role of microbes in human illness
• Pharmaceutical microbiology_ study of microbes related to the
production of antibiotics, enzymes, vaccines, etc
• Food microbiology_ study of microbes causing food spoilage and
foodborne illness
• Agriculture microbiology_ study of agriculturally relevant
microorganisms
APLLIED MICROBIOLOGY

50. • Soil microbiology_ study of organism that are found in the soil.
• Environmental microbiology_ study of the function and diversity of
microbes in their natural environments
• Microbial biotechnology_ the manipulation of microorganism at the
genetic and molecular level to generate useful products
• Industrial microbiology_ the exploitation of microbes for use in
industrial processes e.g. wastewater treatment and industrial
fermentation

51. Facts About Beneficial Bacteria
• The opposite of antibiotics are probiotics - a term coined
in 1965 to describe substances that favor the growth of
beneficial microorganisms in the body.
• Two species of probiotics, Bifidobacterium and
Lactobacillus, have been studied the most.
• Bacteria that produce the enzyme lactase help reduce
lactose intolerance.

52. oMicrobes living in the rumen of the cow are responsible for
the breakdown of the carbohydrate cellulose of plants.
oThe cow lacks the enzymes to break down carbohydrates.
oWithout microbes and their enzymes, ruminants would not be
able to derive any energy or nutrients from a diet of grass.
Microbes enables cows to eat grass?

53. Microbes can degrade explosives?
• Trinitrotoluene, TNT, is a problematic explosive that
contaminates the soil in areas where ammunition is
kept.
• Bacteria named Clostridium bifermentans is able to
break down this contaminant.
• When provided with starch as energy source, the
bacteria can break down the TNT through co-
metabolism by breaking down TNT as a source of
carbon.

54. Bacteria can help clean up oil spills?
• After the Exxon Valdez crashed off the shore of Alaska,
spilling its contents all over the area, one of the biggest
contributors to cleaning up the environment was
Pseudomonas.
• Scientists found that by feeding the contaminated area
with oxygen and waste water, the bacteria present there
were provided with the nutrients needed to flourish,
thereby encouraging the break down of hydrocarbons
within crude oil by Pseudomonas.
• The hydrocarbon that the bacterium feasts on are
converted to carbon dioxide and water.

55. Microbes can make plastics ?
• Alcaligenes eutrophus, is a useful bacterium having the capability of
making plastics.
• The bacterium is able to accomplish this feature because it has
granules that are made of a fat-like polymer and not starch, like
the granules of other bacteria.
• These plastics can be readily degraded and hopefully will pose less
environmental threat.
• There are strong hopes of using these bacteria and their plastics
for medical purposes.

56. Microbes are all over your skin?
• While bacteria are found on your fingers, toes, arms
and legs they are far more numerous on your face.
• are found above and below the surface of your skin and
are in no way harmful.
• The surface of our skin contains over 2 million (2 X
10^6) microbes per square inch.
• A single gram of fecal material, contains over 100
billion (1 X 10^11) bacteria
• A human being consists of approx. 100 trillion (1 X
10^14) cells. Of that number only 10% are mammalian
in origin. The remaining 90% are microbes and together
weigh about one-quarter of a pound. Microbial population
outnumbers human cells

57. Microbes cause body odor?
• The sweat that comes out of your underarms actually does not smell bad.
• The reason that people give off odors when they sweat in their underarms is
that bacteria living there like to eat sweat, and as a result produce waste
products that cause it to smell.
• Body odor can be eliminated by using deoderant.
• Deoderant kills the bacteria under your arms so that it cannot make your
sweat stink.
“So don't forget your deoderant; it does more than just mask
body odor, it stops it before it happens!”

58. How Does Salmonella Get
Inside Chicken Eggs?
• The bacterium actually lives in the feces of chicken.
• Because chickens sit on their eggs, even before they are collected for
consumer purchases, the eggs may be subjected to the bacterium.
• It was found that S. enteritidis could actually penetrate the hard outer shell
of the egg and live inside the yolk, where it can reproduce.
• The bacterium could infect hens' ovaries, and contaminate the egg before it
even developed a shell.

59. Caught Dirty-Handed!!!
• When was the last time you washed your hands?
• Did you use soap?
• What have you done or touched since you washed your hands?
• Have you eaten, put your fingers in your mouth or touched someone
else?
• There are millions of microbes on your hands. Most are naturally
occurring and harmless. But some may be disease-causing germs.
Hand washing with soap lifts off those microbes and rinses them
away.
• Observations in public restrooms reveals what?????
How dirty are
your hands
right now?

60. Importance of Microbiology in medicine
• To understand various infectious agents and the principles underlying
the infection prevention(IP) in health care facilities which has two
primary objectives:
1. To prevent major infections when providing any type of service
that involves invasive procedures (e.g., injections, intravascular
infusions, urinary catheterization, wound management, Intrauterine
device insertion, surgical procedures, etc)
2. To minimize the risk of transmitting serious infections such as
Hepatitis B/C and HIV not only to clients but also to colleagues and
other members of staff such as cleaning and house keeping
personnel
A health practitioner needs to have knowledge in Microbiology to
function effectively and knowledge in the recommended IP
practices which are based on the following principles:

61. • Consider every person (client or staff) infectious
• Wash hands- the most practical procedure for preventing cross-
contamination (person-person)
• Wear gloves before touching anything wet- broken skin, mucous
membranes, blood, body fluids, secretions or excretions
• Use barriers including personal protective equipment (protective
goggles, face masks and aprons) if splashes or spills of any blood,
body fluids, secretions or excretions are anticipated

62. • Use safe work practices- such as not recapping needles, safely
passing sharp instruments, and disposing of sharps in puncture proof
containers
• Process instruments- and other items that come in contact with blood,
body fluids, secretions or excretions (decontaminate, clean, and
sterilize or high-level disinfect them) following recommended IP
practices
• Dispose contaminated instruments and contaminated waste thoroughly
and properly
• Isolate patients- only if secretions or excretions (urine or feces)
cannot be contained

63. Proper infection prevention practices will help a health practitioner to
break the disease transmission cycle in one of the four ways, by:
1. Reducing the number of infection-causing micro-organisms (e.g.,
simple handwashing, cleaning of instrument)
2. Killing or inactivating infection-causing micro-organisms (e.g.,
handwashing with a waterless alcohol preparation, decontamination)
3. Creating barriers to prevent infectious agents from spreading (e.g.,
wearing gloves or personal protective equipment); or
4. Reducing or eliminating risk practices (e.g., hands-free technique,
using disposable gloves and syringes).

64. Microbiology
• will help a health practitioner to understand various modes of
disease transmission such as airborne
• It will help a health practitioner to understand various
precautions to take in order to reduce the risk of nosocomial
transmission of pathogens (e.g., T.B)
• It will help a health practitioner to understand the importance
of management of traffic flow and activity pattern to minimize
the number of micro-organism present in a clean area.
• The number of microorganism in a designated area tends to be
related to the number of people present and their activity

65. Microbiology (cont’d)
• Environmental cleanliness -If fresh air is allowed in
the room it will kill bacteria and retard bacterial
multiplication
• Keep the surrounding clean, free from dust as dust
particles promote bacterial growth
• Ward must be free of insects as insects carry dirt
microorganism to the other places

66. In summary: Role of a health practitioner in
Microbiology
• Asepsis, sterilization, and disinfection
• Recognition of infection
• Infection control—pathogenesis and transmission
• Nosocomial infection
• Immune system
• Clinical thought process

67. 1. What is the difference btwn microbiology & microscope?
2. List the divisions of microbiology
3. Describe the environment, agriculture industrial and health
application of microbiology
4. Explain the germ theory of disease
5. Explain the theory of spontaneous generation & biogenesis
6. List Koch’s postulates of disease
7. What is the importance of microbiology in clinical practice?
A quick recap!

68. Next topic: Classification & Structure of microorganisms